Last updated: 2021-05-04
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Knit directory: QTL_Analysis_Report-Pinkney/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 1b3d712 | Belinda Cornes | 2021-05-04 | Updated Results |
| Rmd | b54e133 | Belinda Cornes | 2021-05-04 | Start workflowr project. |
| abbreviations for strains: | H: het; B: hom B6; C: hom C3A |
| type of cross: | F2 |
| number of mice phenotyped: | 225 |
| total number of mice phenotypes: | 6 |
| phenotypes: | 3 axial length data (R_AVG, L_AVG, Both_AVG); 3 degeneration data (deg_avg_r, deg_avg_l, deg_avg_b) |
| number of mice: | 225 |
| number of markers: | 62 |
| covariates: | sex [F: 120; M: 105] |
R/qtl2 was used (Broman et al, 2019).In this report, we performed QTL mapping for 6 phenotypes for a F2 cross between C3A X B6. Sex did not have a significant effect on eye axial length for any phenotype (after the removal of outliers) .By using the 95% threshold, we identified QTLs that were significant at a genome-wide p value of < 0.05. We estimated effects for each QTL. The QTLs were found for phenotypes as follows:
R_AVG:
L_AVG:
Both_AVG:
deg_avg_r:
deg_avg_l:
deg_avg_b:
Broman, K. W., Wu H., Sen S., Churchill, G. A. 2003. R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890.
Doerge, R. W. and Churchill, G. A.. 1996. Permutation tests for multiple loci affecting a quantitative character. Genetics 142, 285-294.
Lander, E. and Kruglyak, L.. 1995. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics.11: 241-247.
Sen, S. and Churchill, G. A.. 2001. A statistical framework for quantitative trait mapping. Genetics 159, 371-387. 12
Broman, K. W., Gatti, D. M. Churchill, G. A.2019. R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations. Genetics 211, 2 495-502
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] ggrepel_0.8.2 qtlcharts_0.11-6 qtl2_0.22 broman_0.70-4
[5] ggplot2_3.3.2 tibble_3.0.1 readxl_1.3.1 cluster_2.1.0
[9] dplyr_0.8.5 optparse_1.6.6 mclust_5.4.6 tidyr_1.0.2
[13] data.table_1.12.8 knitr_1.28 kableExtra_1.1.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.0.0 xfun_0.13 purrr_0.3.4 colorspace_1.4-1
[5] vctrs_0.3.1 htmltools_0.4.0 getopt_1.20.3 viridisLite_0.3.0
[9] yaml_2.2.1 blob_1.2.1 rlang_0.4.6 later_1.0.0
[13] pillar_1.4.4 DBI_1.1.0 glue_1.4.1 withr_2.2.0
[17] bit64_0.9-7 lifecycle_0.2.0 stringr_1.4.0 munsell_0.5.0
[21] gtable_0.3.0 cellranger_1.1.0 rvest_0.3.5 memoise_1.1.0
[25] evaluate_0.14 httpuv_1.5.2 parallel_3.6.2 Rcpp_1.0.4.6
[29] readr_1.3.1 promises_1.1.0 scales_1.1.1 backports_1.1.7
[33] jsonlite_1.6.1 webshot_0.5.2 bit_1.1-15.2 fs_1.4.1
[37] hms_0.5.3 digest_0.6.25 stringi_1.4.6 rprojroot_1.3-2
[41] grid_3.6.2 tools_3.6.2 magrittr_1.5 RSQLite_2.2.0
[45] crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.1
[49] xml2_1.3.1 assertthat_0.2.1 rmarkdown_2.1 httr_1.4.1
[53] rstudioapi_0.11 qtl_1.46-2 R6_2.4.1 git2r_0.26.1
[57] compiler_3.6.2