Last updated: 2022-04-06
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Knit directory: Serreze-T1D_Workflow/
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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
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.
There are no past versions. Publish this analysis with wflow_publish()
to start tracking its development.
load("data/gm_allqc_5.batches.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 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
pr <- readRDS("data/serreze_probs_allqc_5.batches.rds")
#pr <- readRDS("data/serreze_probs.rds")
geno <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/sample_geno_bc.csv", as.is=T)
names(geno) <- gsub("\\.","-",names(geno))
rownames(geno) <- geno$marker
## extracting animals with ici and pbs group status
miceinfo <- gm$covar[gm$covar$group == "PBS" | gm$covar$group == "ICI",]
table(miceinfo$group)
ICI PBS
104 34
mice.ids <- rownames(miceinfo)
gm <- gm[mice.ids]
gm
Object of class cross2 (crosstype "bc")
Total individuals 138
No. genotyped individuals 138
No. phenotyped individuals 138
No. with both geno & pheno 138
No. phenotypes 1
No. covariates 6
No. phenotype covariates 0
No. chromosomes 20
Total markers 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
table(gm$covar$group)
ICI PBS
104 34
covars <- read_csv("data/covar_corrected_ici.vs.pbs_5.batches.csv")
# removing any missing info
#covars <- subset(covars, covars$age.of.onset!='')
nrow(covars)
[1] 138
table(covars$group)
ICI PBS
104 34
# keeping only informative mice
gm <- gm[covars$Mouse.ID]
gm
Object of class cross2 (crosstype "bc")
Total individuals 138
No. genotyped individuals 138
No. phenotyped individuals 138
No. with both geno & pheno 138
No. phenotypes 1
No. covariates 6
No. phenotype covariates 0
No. chromosomes 20
Total markers 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
table(gm$covar$group)
ICI PBS
104 34
pr.qc.ids <- pr
for (i in 1:20){pr.qc.ids[[i]] = pr.qc.ids[[i]][covars$Mouse.ID,,]}
geno <- geno[,covars$Mouse.ID]
geno <- geno[marker_names(gm),]
dim(geno)
[1] 34537 138
## calculating genotype frequencies
### from geno genotypes
g <- do.call("cbind", gm$geno)
gf_mar_geno <- t(apply(g, 2, function(a) table(factor(a, 1:2))/sum(a != 0)))
gn_mar_geno <- t(apply(g, 2, function(a) table(factor(a, 0:2))))
#gf_mar_raw<- gf_mar_raw[gf_mar_raw[,2] != "NaN",]
colnames(gf_mar_geno) <- c("freq_AA_geno_table","freq_AB_geno_table")
colnames(gn_mar_geno) <- c("count_missing_geno_table","count_AA_geno_table","count_AB_geno_table")
gfn_mar_geno <- merge(as.data.frame(gn_mar_geno), as.data.frame(gf_mar_geno), by="row.names")
rownames(gfn_mar_geno) <- gfn_mar_geno[,1]
gfn_mar_geno <- gfn_mar_geno[-1]
### from raw using table function in R
#genosl <- list()
#for(i in 1:nrow(geno)){
##for(i in 1:3){
# genoi <- geno[i,]
# freqf <- table(factor(geno[i,], c("-","AA","AB")))
# genoi$count_AA_raw_rowSums <- rowSums(genoi == "AA")
# genoi$count_AB_raw_rowSums <- rowSums(genoi == "AB")
# genoi$count_missing_raw_rowSums <- rowSums(genoi == "-")
# freqf <- t(table(factor(geno[i,], c("-","AA","AB"))))
# freqf <- as.data.frame(t(freqf[1,]))
# rownames(freqf) <- rownames(genoi)
# colnames(freqf) <- c("count_missing_raw_table","count_AA_raw_table","count_AB_raw_table")
# genoif <- cbind(freqf,genoi[c("count_AA_raw_rowSums","count_AB_raw_rowSums","count_missing_raw_rowSums")])
# genosl[[i]] = genoif
#}
#gf_mar_raw <- do.call("rbind",genosl)
#gf_mar_raw <- gf_mar_raw[,c(1:3,6,4:5)]
#gf_mar_raw$index <- 1:nrow(gf_mar_raw)
### from probabilities
gf_mar_probs.1 <- calc_geno_freq(pr.qc.ids, by = "marker", omit_x = FALSE)
#gn_mar_probs <- calc_geno_freq(probs, by = "individual", omit_x = FALSE)
gf_mar_probs <- rbind(gf_mar_probs.1$A[,1:2], gf_mar_probs.1$X[,1:2])
colnames(gf_mar_probs) <- paste0("freq_",colnames(gf_mar_probs),"_probs")
gf_mar_probs <- as.data.frame(gf_mar_probs)
gf_mar_probs$index <- 1:nrow(gf_mar_probs)
### merging all genotype frequecies for all markers
#gf_mar.1 <- merge(as.data.frame(gf_mar_raw), as.data.frame(gfn_mar_geno), by="row.names")
#rownames(gf_mar.1) <- gf_mar.1[,1]
#gf_mar.1 <- gf_mar.1[-1]
#gf_mar <- merge(gf_mar.1,as.data.frame(gf_mar_probs), by="row.names")
gf_mar <- merge(as.data.frame(gfn_mar_geno),as.data.frame(gf_mar_probs), by="row.names")
rownames(gf_mar) <- gf_mar[,1]
gf_mar <- gf_mar[-1]
gf_mar <- gf_mar[order(gf_mar$index),]
dim(gf_mar)
[1] 34537 8
# Calculating ratio and flagging informative marker
gf_mar$ratio = as.numeric(gf_mar$freq_AA_geno_table)/as.numeric(gf_mar$freq_AB_geno_table)
gf_mar$Include = ifelse(gf_mar$ratio >= 0.90 & gf_mar$ratio <= 1.10, TRUE,FALSE)
table(gf_mar$Include)
FALSE TRUE
27981 6556
## filtering out <= 0.05
gf_mar$count.geno <- rowSums(gf_mar[c("freq_AA_geno_table","freq_AB_geno_table")] <=0.05)
filtered_gf_mar_geno <- gf_mar[gf_mar$count.geno != 1,]
filtered_gf_mar_geno <- filtered_gf_mar_geno[,-which(names(filtered_gf_mar_geno) %in% c("count.geno","index"))]
dim(filtered_gf_mar_geno)
[1] 26548 9
table(filtered_gf_mar_geno$Include)
FALSE TRUE
19992 6556
gf_mar$count.probs <- rowSums(gf_mar[c("freq_AA_probs","freq_AB_probs")] <=0.05)
filtered_gf_mar_probs <- gf_mar[gf_mar$count.probs != 1,]
filtered_gf_mar_probs <- filtered_gf_mar_probs[,-which(names(filtered_gf_mar_probs) %in% c("count.geno","count.probs","index"))]
dim(filtered_gf_mar_probs)
[1] 27826 9
table(filtered_gf_mar_probs$Include)
FALSE TRUE
21276 6550
## merging with sample_genos
#filtered_gf_mar_geno_sample <- merge(geno,filtered_gf_mar_geno, by="row.names", all.y=T)
#filtered_gf_mar_geno_sample <- filtered_gf_mar_geno_sample[order(filtered_gf_mar_geno_sample$index),]
#filtered_gf_mar_geno_sample <- filtered_gf_mar_geno_sample[,-which(names(filtered_gf_mar_geno_sample) %in% c("count.geno","index"))]
#names(filtered_gf_mar_geno_sample)[1] <- c("marker")
#dim(filtered_gf_mar_geno_sample)
#filtered_gf_mar_probs_sample <- merge(geno,filtered_gf_mar_probs, by="row.names", all.y=T)
#filtered_gf_mar_probs_sample <- filtered_gf_mar_probs_sample[order(filtered_gf_mar_probs_sample$index),]
#filtered_gf_mar_probs_sample <- filtered_gf_mar_probs_sample[,-which(names(filtered_gf_mar_probs_sample) %in% c("count.geno","count.probs","index"))]
#names(filtered_gf_mar_probs_sample)[1] <- c("marker")
#dim(filtered_gf_mar_probs_sample)
## saving files
#write.csv(filtered_gf_mar_geno_sample, "data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed.csv", quote=F)
#write.csv(filtered_gf_mar_probs_sample, "data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed.csv", quote=F)
write.csv(filtered_gf_mar_geno, "data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_5.batches.csv", quote=F)
write.csv(filtered_gf_mar_probs, "data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_5.batches.csv", quote=F)
load("data/gm_allqc_5.batches.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 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
pr <- readRDS("data/serreze_probs_allqc_5.batches.rds")
#pr <- readRDS("data/serreze_probs.rds")
geno <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/sample_geno_bc.csv", as.is=T)
names(geno) <- gsub("\\.","-",names(geno))
rownames(geno) <- geno$marker
## extracting animals with ici and pbs group status
miceinfo <- gm$covar[gm$covar$group == "PBS" | gm$covar$group == "ICI",]
table(miceinfo$group)
ICI PBS
104 34
mice.ids <- rownames(miceinfo)
gm <- gm[mice.ids]
gm
Object of class cross2 (crosstype "bc")
Total individuals 138
No. genotyped individuals 138
No. phenotyped individuals 138
No. with both geno & pheno 138
No. phenotypes 1
No. covariates 6
No. phenotype covariates 0
No. chromosomes 20
Total markers 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
table(gm$covar$group)
ICI PBS
104 34
covars <- read_csv("data/covar_corrected.cleaned_ici.vs.pbs_5.batches.csv")
# removing any missing info
covars <- subset(covars, covars$age.of.onset!='')
nrow(covars)
[1] 138
table(covars$group)
ICI PBS
104 34
# keeping only informative mice
gm <- gm[covars$Mouse.ID]
gm
Object of class cross2 (crosstype "bc")
Total individuals 138
No. genotyped individuals 138
No. phenotyped individuals 138
No. with both geno & pheno 138
No. phenotypes 1
No. covariates 6
No. phenotype covariates 0
No. chromosomes 20
Total markers 34537
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257 935
17 18 19 X
501 913 1014 4532
table(gm$covar$group)
ICI PBS
104 34
pr.qc.ids <- pr
for (i in 1:20){pr.qc.ids[[i]] = pr.qc.ids[[i]][covars$Mouse.ID,,]}
geno <- geno[,covars$Mouse.ID]
geno <- geno[marker_names(gm),]
dim(geno)
[1] 34537 138
## calculating genotype frequencies
### from geno genotypes
g <- do.call("cbind", gm$geno)
gf_mar_geno <- t(apply(g, 2, function(a) table(factor(a, 1:2))/sum(a != 0)))
gn_mar_geno <- t(apply(g, 2, function(a) table(factor(a, 0:2))))
#gf_mar_raw<- gf_mar_raw[gf_mar_raw[,2] != "NaN",]
colnames(gf_mar_geno) <- c("freq_AA_geno_table","freq_AB_geno_table")
colnames(gn_mar_geno) <- c("count_missing_geno_table","count_AA_geno_table","count_AB_geno_table")
gfn_mar_geno <- merge(as.data.frame(gn_mar_geno), as.data.frame(gf_mar_geno), by="row.names")
rownames(gfn_mar_geno) <- gfn_mar_geno[,1]
gfn_mar_geno <- gfn_mar_geno[-1]
### from raw using table function in R
#genosl <- list()
#for(i in 1:nrow(geno)){
##for(i in 1:3){
# genoi <- geno[i,]
# freqf <- table(factor(geno[i,], c("-","AA","AB")))
# genoi$count_AA_raw_rowSums <- rowSums(genoi == "AA")
# genoi$count_AB_raw_rowSums <- rowSums(genoi == "AB")
# genoi$count_missing_raw_rowSums <- rowSums(genoi == "-")
# freqf <- t(table(factor(geno[i,], c("-","AA","AB"))))
# freqf <- as.data.frame(t(freqf[1,]))
# rownames(freqf) <- rownames(genoi)
# colnames(freqf) <- c("count_missing_raw_table","count_AA_raw_table","count_AB_raw_table")
# genoif <- cbind(freqf,genoi[c("count_AA_raw_rowSums","count_AB_raw_rowSums","count_missing_raw_rowSums")])
# genosl[[i]] = genoif
#}
#gf_mar_raw <- do.call("rbind",genosl)
#gf_mar_raw <- gf_mar_raw[,c(1:3,6,4:5)]
#gf_mar_raw$index <- 1:nrow(gf_mar_raw)
### from probabilities
gf_mar_probs.1 <- calc_geno_freq(pr.qc.ids, by = "marker", omit_x = FALSE)
#gn_mar_probs <- calc_geno_freq(probs, by = "individual", omit_x = FALSE)
gf_mar_probs <- rbind(gf_mar_probs.1$A[,1:2], gf_mar_probs.1$X[,1:2])
colnames(gf_mar_probs) <- paste0("freq_",colnames(gf_mar_probs),"_probs")
gf_mar_probs <- as.data.frame(gf_mar_probs)
gf_mar_probs$index <- 1:nrow(gf_mar_probs)
### merging all genotype frequecies for all markers
#gf_mar.1 <- merge(as.data.frame(gf_mar_raw), as.data.frame(gfn_mar_geno), by="row.names")
#rownames(gf_mar.1) <- gf_mar.1[,1]
#gf_mar.1 <- gf_mar.1[-1]
#gf_mar <- merge(gf_mar.1,as.data.frame(gf_mar_probs), by="row.names")
gf_mar <- merge(as.data.frame(gfn_mar_geno),as.data.frame(gf_mar_probs), by="row.names")
rownames(gf_mar) <- gf_mar[,1]
gf_mar <- gf_mar[-1]
gf_mar <- gf_mar[order(gf_mar$index),]
dim(gf_mar)
[1] 34537 8
# Calculating ratio and flagging informative marker
gf_mar$ratio = as.numeric(gf_mar$freq_AA_geno_table)/as.numeric(gf_mar$freq_AB_geno_table)
gf_mar$Include = ifelse(gf_mar$ratio >= 0.90 & gf_mar$ratio <= 1.10, TRUE,FALSE)
table(gf_mar$Include)
FALSE TRUE
27981 6556
## filtering out <= 0.05
gf_mar$count.geno <- rowSums(gf_mar[c("freq_AA_geno_table","freq_AB_geno_table")] <=0.05)
filtered_gf_mar_geno <- gf_mar[gf_mar$count.geno != 1,]
filtered_gf_mar_geno <- filtered_gf_mar_geno[,-which(names(filtered_gf_mar_geno) %in% c("count.geno","index"))]
dim(filtered_gf_mar_geno)
[1] 26548 9
table(filtered_gf_mar_geno$Include)
FALSE TRUE
19992 6556
gf_mar$count.probs <- rowSums(gf_mar[c("freq_AA_probs","freq_AB_probs")] <=0.05)
filtered_gf_mar_probs <- gf_mar[gf_mar$count.probs != 1,]
filtered_gf_mar_probs <- filtered_gf_mar_probs[,-which(names(filtered_gf_mar_probs) %in% c("count.geno","count.probs","index"))]
dim(filtered_gf_mar_probs)
[1] 27826 9
table(filtered_gf_mar_probs$Include)
FALSE TRUE
21276 6550
## merging with sample_genos
#filtered_gf_mar_geno_sample <- merge(geno,filtered_gf_mar_geno, by="row.names", all.y=T)
#filtered_gf_mar_geno_sample <- filtered_gf_mar_geno_sample[order(filtered_gf_mar_geno_sample$index),]
#filtered_gf_mar_geno_sample <- filtered_gf_mar_geno_sample[,-which(names(filtered_gf_mar_geno_sample) %in% c("count.geno","index"))]
#names(filtered_gf_mar_geno_sample)[1] <- c("marker")
#dim(filtered_gf_mar_geno_sample)
#filtered_gf_mar_probs_sample <- merge(geno,filtered_gf_mar_probs, by="row.names", all.y=T)
#filtered_gf_mar_probs_sample <- filtered_gf_mar_probs_sample[order(filtered_gf_mar_probs_sample$index),]
#filtered_gf_mar_probs_sample <- filtered_gf_mar_probs_sample[,-which(names(filtered_gf_mar_probs_sample) %in% c("count.geno","count.probs","index"))]
#names(filtered_gf_mar_probs_sample)[1] <- c("marker")
#dim(filtered_gf_mar_probs_sample)
## saving files
#write.csv(filtered_gf_mar_geno_sample, "data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv", quote=F)
#write.csv(filtered_gf_mar_probs_sample, "data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv", quote=F)
write.csv(filtered_gf_mar_geno, "data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_5.batches.csv", quote=F)
write.csv(filtered_gf_mar_probs, "data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches.csv", quote=F)
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] getopt_1.20.3 later_1.0.0 git2r_0.26.1 generics_0.0.2
[29] ellipsis_0.3.2 cachem_1.0.5 withr_2.4.2 cli_3.0.0
[33] mnormt_1.5-7 magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0
[37] evaluate_0.14 fs_1.4.1 fansi_0.5.0 nlme_3.1-142
[41] xml2_1.3.1 tools_3.6.2 hms_0.5.3 lifecycle_1.0.1
[45] stringr_1.4.0 Rhdf5lib_1.6.3 munsell_0.5.0 compiler_3.6.2
[49] rlang_1.0.2 grid_3.6.2 rstudioapi_0.13 rmarkdown_2.1
[53] gtable_0.3.0 DBI_1.1.1 R6_2.5.0 fastmap_1.1.0
[57] bit_4.0.4 utf8_1.2.1 rprojroot_1.3-2 readr_1.3.1
[61] stringi_1.7.2 parallel_3.6.2 Rcpp_1.0.7 vctrs_0.3.8
[65] tidyselect_1.1.2 xfun_0.24