QTL Analysis - age of onset [ICI-Early vs PBS] (corrected phenotype with outliers removed if any)

workflowr

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Last updated: 2022-04-14

Checks: 5 2

Knit directory: Serreze-T1D_Workflow/

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Repository version: a8c2d1a

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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-11_peak.marker-UNC19970181_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-11_peak.marker-UNC20090524_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-13_peak.marker-UNCHS036773_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-14_peak.marker-UNC24056202_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-17_peak.marker-UNCJPD006614_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-2_peak.marker-UNC4609527_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008219_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008229_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008271_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008432_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008627_lod.drop-1.5_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_rz.age-no.covariates_blup_sub_chr-9_peak.marker-UNC17203597_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-UNCHS020486_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-JAX00153527_lod.drop-1.5_5.batches.csv
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    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-UNCHS020443_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-UNCHS020486_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed.csv
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    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.pbs_scanone_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches_mis.Rdata
    Untracked:  data/percent_missing_id_3.batches.RData
    Untracked:  data/percent_missing_id_4.batches.RData
    Untracked:  data/percent_missing_id_4.batches_bc.RData
    Untracked:  data/percent_missing_id_5.batches.RData
    Untracked:  data/percent_missing_marker_4.batches.RData
    Untracked:  data/percent_missing_marker_5.batches.RData
    Untracked:  data/pheno.csv
    Untracked:  data/pheno_BC312.csv
    Untracked:  data/physical_map.csv
    Untracked:  data/physical_map_BC312.csv
    Untracked:  data/qc_info_bad_sample_3.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches_bc.RData
    Untracked:  data/qc_info_bad_sample_5.batches.RData
    Untracked:  data/remaining.markers_geno.freq.xlsx
    Untracked:  data/sample_geno.csv
    Untracked:  data/sample_geno_AHB_BC312.csv
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    Untracked:  data/sample_geno_bc_BC312.csv
    Untracked:  data/serreze_probs.rds
    Untracked:  data/serreze_probs_BC312.rds
    Untracked:  data/serreze_probs_allqc.rds
    Untracked:  data/serreze_probs_allqc_5.batches.rds
    Untracked:  data/serreze_probs_allqc_5.batches_mis.rds
    Untracked:  data/summary.cg_3.batches.RData
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    Untracked:  output/Percent_missing_genotype_data_per_marker_5.batches.pdf
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    Untracked:  output/genotype_error_marker_5.batches.pdf
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Unstaged changes:
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/index_5.batches.Rmd
    Modified:   analysis/index_5.batches_additional.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd) and HTML (docs/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	a8c2d1a	Belinda Cornes	2022-04-13	additonal analysis - peaks and continuous variables
html	a8c2d1a	Belinda Cornes	2022-04-13	additonal analysis - peaks and continuous variables

---

Loading Data

load("data/gm_allqc_5.batches_mis.RData")

#gm_allqc
gm=gm_allqc
gm

Object of class cross2 (crosstype "bc")

Total individuals               308
No. genotyped individuals       308
No. phenotyped individuals      308
No. with both geno & pheno      308

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131356

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7586 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#removing ici-late
table(gm$covar$group)

 (A2 Parental) (DQ8 Parental) B6.g7 Parental            EOI             F1 
             2              2              1            164              1 
           ICI            PBS 
           104             34 

table(gm$covar$"diabetic status")

  Both Projects   Diabetes Proj ICI-No Diabetes     Myocarditis      Spont. T1D 
              1               3             164               2              34 
        T1D <17          T1D<17          T1D>17 
             36              51              17 

ici.late_ids <- gm$covar[gm$covar$"diabetic status" == "T1D>17",]$id
length(ici.late_ids)

[1] 17

ici.late_ids

 [1] "NG00198-ICI-LATE" "NG00329-ICI-LATE" "NG00343-ICI-LATE" "NG00386-ICI-LATE"
 [5] "NG00442-ICI-LATE" "NG00443-ICI-LATE" "NG00526-ICI-LATE" "NG00522-ICI-LATE"
 [9] "NG00790-ICI-LATE" "NG00874-ICI-LATE" "NG00929-ICI-LATE" "NG01225-ICI-LATE"
[13] "NG01303-ICI-LATE" "NG01020-ICI-LATE" "NG01397-ICI-LATE" "NG01389-ICI-LATE"
[17] "NG01548-ICI-LATE"

gm <- gm[paste0("-",as.character(ici.late_ids)),]
table(gm$covar$"diabetic status")

  Both Projects   Diabetes Proj ICI-No Diabetes     Myocarditis      Spont. T1D 
              1               3             164               2              34 
        T1D <17          T1D<17 
             36              51 

##extracting animals with ici-early and pbs group status
miceinfo <- gm$covar[gm$covar$group == "PBS" | gm$covar$group == "ICI",]
table(miceinfo$group)

ICI PBS 
 87  34 

mice.ids <- rownames(miceinfo)

gm <- gm[mice.ids]
gm

Object of class cross2 (crosstype "bc")

Total individuals               121
No. genotyped individuals       121
No. phenotyped individuals      121
No. with both geno & pheno      121

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131356

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7586 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

table(gm$covar$group)

ICI PBS 
 87  34 

gm.full <- gm



covars <- read_csv("data/covar_corrected.cleaned_ici-early.vs.pbs_5.batches_mis.csv")
#removing any missing info
missing_ids <- covars[which(covars$"age.of.onset"==""),]$Mouse.ID
length(missing_ids)

[1] 0

missing_ids

character(0)

if(length(missing_ids) != 0){
gm <- gm[paste0("-",as.character(missing_ids)),]
gm
table(gm$covar$group)

#keeping only mouseids in covars
covars <- covars[gm$covar$id,]
table(covars$group)
}

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")


##removing problmetic marker

gm <- drop_markers(gm, "UNCHS013106")

#pmap_interp = interp_map(map, gm$gmap, gm$pmap)
markers <- marker_names(gm)
gmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/genetic_map.csv")
pmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/physical_map.csv")
#mapdf <- merge(gmapdf,pmapdf, by=c("marker","chr"), all=T)
#rownames(mapdf) <- mapdf$marker
#mapdf <- mapdf[markers,]
#names(mapdf) <- c('marker','chr','gmapdf','pmapdf')
#mapdfnd <- mapdf[!duplicated(mapdf[c(2:3)]),]

pr.qc <- calc_genoprob(gm)

gm

Object of class cross2 (crosstype "bc")

Total individuals               121
No. genotyped individuals       121
No. phenotyped individuals      121
No. with both geno & pheno      121

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131355

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

Preparing necessary info

covars$age.of.onset <- as.numeric(covars$age.of.onset)
Xcovar <- get_x_covar(gm)
addcovar = model.matrix(~ICI_Early.vs.PBS, data = covars)[,-1]
#addcovar.i = model.matrix(~ICI_Early.vs.PBS, data = covars)[,-1]

K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

No additive covariates

Significance thresholds

operm <- scan1perm(pr.qc, covars["age.of.onset"], model="normal", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap))

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	5.731245	6.112502
0.05	5.421283	5.821758
0.1	5.032869	5.441556

Genome-wide scan

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
#par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - ICI-Early vs. PBS (no covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


print("with no kinship")

[1] “with no kinship”

outf <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal")

plot_lod(outf,gm$gmap)

print("with normal kinship")

[1] “with normal kinship”

outk <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", kinship=kinship)

plot_lod(outk,gm$gmap)

print("with loco kinship")

[1] “with loco kinship”

out <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", kinship=K)

plot_lod(out,gm$gmap)

print(paste0("number of samples in analysis = ", as.data.frame(attributes(out)$sample_size)[1,]))

[1] “number of samples in analysis = 121”

LOD peaks

Centimorgan (cM)

peaks<-find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)


if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (no covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 5.03286885886213 [autosomes]/5.44155598859186 [x-chromosome]”

Megabase (MB)

peaks_mba<-find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

  plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (no covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 5.03286885886213 [autosomes]/5.44155598859186 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, covars[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], covars[peaks$phenotype[i]])
  blup_sub <- scan1blup(pr_sub[,chr], covars[peaks$phenotype[i]])

  write.csv(as.data.frame(blup_sub), paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-no.covariates_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM] )")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM] )")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM] )")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-no.covariates_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 5.03286885886213 [autosomes]/5.44155598859186 [x-chromosome]”

Additive covariates

Significance thresholds

operm <- scan1perm(pr.qc, covars["age.of.onset"], model="normal", addcovar=addcovar, n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap))

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	5.863142	6.579023
0.05	5.454684	6.183736
0.1	4.942844	5.666823

Genome-wide scan

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
#par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - ICI-Early vs. PBS (ith additive covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


print("with no kinship")

[1] “with no kinship”

outfa <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar)

plot_lod(outfa,gm$gmap)

print("with normal kinship")

[1] “with normal kinship”

outka <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar, kinship=kinship)

plot_lod(outka,gm$gmap)

print("with loco kinship")

[1] “with loco kinship”

outa <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar, kinship=K)

plot_lod(outa,gm$gmap)

out = outa

print(paste0("number of samples in analysis = ", as.data.frame(attributes(out)$sample_size)[1,]))

[1] “number of samples in analysis = 121”

LOD peaks

Centimorgan (cM)

peaks<-find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (with additive covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 4.94284385503285 [autosomes]/5.66682315406148 [x-chromosome]”

Megabase (MB)

peaks_mba<-find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (with additive covariates) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 4.94284385503285 [autosomes]/5.66682315406148 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, covars[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], covars[peaks$phenotype[i]])
  blup_sub <- scan1blup(pr_sub[,chr], covars[peaks$phenotype[i]])

  write.csv(as.data.frame(blup_sub), paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-additive.covariates_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM] )")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM] )")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM] )")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-additive.covariates_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}
} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 4.94284385503285 [autosomes]/5.66682315406148 [x-chromosome]”

Interactive term

Significance thresholds

operm <- scan1perm(pr.qc, covars["age.of.onset"], model="normal", addcovar=addcovar, intcovar=addcovar, n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap))

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	16.50118	11.91601
0.05	15.53988	11.77544
0.1	14.33526	11.59163

Genome-wide scan

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
#par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - ICI-Early vs. PBS (with interactive covariate) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


print("with no kinship")

[1] “with no kinship”

outfi <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar, intcovar=addcovar)

plot_lod(outfi,gm$gmap)

outf.new <- outfi-outfa

plot_lod(outf.new,gm$gmap)

print("with normal kinship")

[1] “with normal kinship”

outki <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar, intcovar=addcovar, kinship=kinship)

plot_lod(outki,gm$gmap)

outk.new <- outki-outka

plot_lod(outk.new,gm$gmap)

print("with loco kinship")

[1] “with loco kinship”

outi <- scan1(pr.qc, covars["age.of.onset"], Xcovar=Xcovar, model="normal", addcovar=addcovar, intcovar=addcovar, kinship=K)

plot_lod(outi,gm$gmap)

outi.new <- outi-outa

plot_lod(outi.new,gm$gmap)

out = outi.new


print(paste0("number of samples in analysis = ", as.data.frame(attributes(out)$sample_size)[1,]))

[1] “number of samples in analysis = 121”

LOD peaks

Centimorgan (cM)

peaks<-find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (with interactive covariate) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 14.3352646485302 [autosomes]/11.5916265309319 [x-chromosome]”

Megabase (MB)

peaks_mba<-find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.1)$A, thresholdX = summary(operm,alpha=0.1)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " - ICI-Early vs. PBS (with interactive covariate) [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 14.3352646485302 [autosomes]/11.5916265309319 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, covars[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], covars[peaks$phenotype[i]])
  blup_sub <- scan1blup(pr_sub[,chr], covars[peaks$phenotype[i]])

  write.csv(as.data.frame(blup_sub), paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-interactive.covariate_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM] )")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM] )")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM] )")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici-early.vs.pbs_",peaks$phenotype[i],"-interactive.covariate_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}
} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.1) level of ",summary(operm,alpha=0.1)$A, " [autosomes]/",summary(operm,alpha=0.1)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.1) level of 14.3352646485302 [autosomes]/11.5916265309319 [x-chromosome]”

Session information

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] abind_1.4-5       qtl2_0.22         reshape2_1.4.4    ggplot2_3.3.5    
 [5] tibble_3.1.2      psych_2.0.7       readxl_1.3.1      cluster_2.1.0    
 [9] dplyr_1.0.8       optparse_1.6.6    rhdf5_2.28.1      mclust_5.4.6     
[13] tidyr_1.0.2       data.table_1.14.0 knitr_1.33        kableExtra_1.1.0 
[17] workflowr_1.6.2  

loaded via a namespace (and not attached):
 [1] httr_1.4.1        bit64_4.0.5       viridisLite_0.4.0 assertthat_0.2.1 
 [5] highr_0.9         blob_1.2.1        cellranger_1.1.0  yaml_2.2.1       
 [9] pillar_1.6.1      RSQLite_2.2.7     backports_1.2.1   lattice_0.20-38  
[13] glue_1.4.2        digest_0.6.27     promises_1.1.0    rvest_0.3.5      
[17] colorspace_2.0-2  htmltools_0.5.1.1 httpuv_1.5.2      plyr_1.8.6       
[21] pkgconfig_2.0.3   purrr_0.3.4       scales_1.1.1      webshot_0.5.2    
[25] whisker_0.4       getopt_1.20.3     later_1.0.0       git2r_0.26.1     
[29] generics_0.0.2    ellipsis_0.3.2    cachem_1.0.5      withr_2.4.2      
[33] cli_3.0.0         mnormt_1.5-7      magrittr_2.0.1    crayon_1.4.1     
[37] memoise_2.0.0     evaluate_0.14     fs_1.4.1          fansi_0.5.0      
[41] nlme_3.1-142      xml2_1.3.1        tools_3.6.2       hms_0.5.3        
[45] lifecycle_1.0.1   stringr_1.4.0     Rhdf5lib_1.6.3    munsell_0.5.0    
[49] compiler_3.6.2    rlang_1.0.2       grid_3.6.2        rstudioapi_0.13  
[53] rmarkdown_2.1     gtable_0.3.0      DBI_1.1.1         R6_2.5.0         
[57] fastmap_1.1.0     bit_4.0.4         utf8_1.2.1        rprojroot_1.3-2  
[61] readr_1.3.1       stringi_1.7.2     parallel_3.6.2    Rcpp_1.0.7       
[65] vctrs_0.3.8       tidyselect_1.1.2  xfun_0.24