Last updated: 2022-02-10
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Knit directory: Serreze-T1D_Workflow/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 9afdeb5 | Belinda Cornes | 2022-02-10 | preparing data |
load("data/gm_allqc_4.batches.RData")
gm_allqcObject of class cross2 (crosstype "bc")
Total individuals 188
No. genotyped individuals 188
No. phenotyped individuals 188
No. with both geno & pheno 188
No. phenotypes 1
No. covariates 6
No. phenotype covariates 0
No. chromosomes 20
Total markers 131578
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13
9977 10005 7858 7589 7621 7758 7413 6472 6725 6396 7154 6137 6085
14 15 16 17 18 19 X
5981 5346 5019 5093 4607 3564 4778 pr <- calc_genoprob(gm_allqc)
saveRDS(pr, file = "data/serreze_probs_allqc.rds")
sessionInfo()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_0.8.5 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] ellipsis_0.3.2 cachem_1.0.5 withr_2.4.2 mnormt_1.5-7
[33] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0 evaluate_0.14
[37] fs_1.4.1 fansi_0.5.0 nlme_3.1-142 xml2_1.3.1
[41] tools_3.6.2 hms_0.5.3 lifecycle_1.0.0 stringr_1.4.0
[45] Rhdf5lib_1.6.3 munsell_0.5.0 compiler_3.6.2 rlang_0.4.11
[49] grid_3.6.2 rstudioapi_0.13 rmarkdown_2.1 gtable_0.3.0
[53] DBI_1.1.1 R6_2.5.0 fastmap_1.1.0 bit_4.0.4
[57] utf8_1.2.1 rprojroot_1.3-2 readr_1.3.1 stringi_1.7.2
[61] parallel_3.6.2 Rcpp_1.0.7 vctrs_0.3.8 tidyselect_1.0.0
[65] xfun_0.24