Last updated: 2023-01-11
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Unstaged changes:
Modified: analysis/index_5.batches.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_4.batches_myo.RData")
gm_allqcObject of class cross2 (crosstype "bc")
Total individuals 208
No. genotyped individuals 208
No. phenotyped individuals 208
No. with both geno & pheno 208
No. phenotypes 1
No. covariates 11
No. phenotype covariates 0
No. chromosomes 20
Total markers 32610
No. markers by chr:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2498 2407 1748 1770 1649 1835 1544 1515 1773 1102 1744 1214 1442 1497 1109 835
17 18 19 X
674 813 940 4501 pr <- calc_genoprob(gm_allqc)
saveRDS(pr, file = "data/serreze_probs_allqc_4.batches_myo.rds")
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] abind_1.4-5 qtl2_0.30 reshape2_1.4.4 ggplot2_3.4.0
[5] tibble_3.1.8 psych_2.2.9 readxl_1.4.1 cluster_2.1.4
[9] dplyr_1.0.10 optparse_1.7.3 rhdf5_2.40.0 mclust_6.0.0
[13] tidyr_1.2.1 data.table_1.14.6 knitr_1.41 kableExtra_1.3.4
[17] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] httr_1.4.4 sass_0.4.4 bit64_4.0.5 jsonlite_1.8.4
[5] viridisLite_0.4.1 bslib_0.4.1 assertthat_0.2.1 getPass_0.2-2
[9] highr_0.9 blob_1.2.3 cellranger_1.1.0 yaml_2.3.6
[13] pillar_1.8.1 RSQLite_2.2.19 lattice_0.20-45 glue_1.6.2
[17] digest_0.6.30 promises_1.2.0.1 rvest_1.0.3 colorspace_2.0-3
[21] htmltools_0.5.3 httpuv_1.6.6 plyr_1.8.8 pkgconfig_2.0.3
[25] purrr_0.3.5 scales_1.2.1 webshot_0.5.4 processx_3.8.0
[29] svglite_2.1.0 whisker_0.4.1 getopt_1.20.3 later_1.3.0
[33] git2r_0.30.1 generics_0.1.3 cachem_1.0.6 withr_2.5.0
[37] cli_3.4.1 mnormt_2.1.1 magrittr_2.0.3 memoise_2.0.1
[41] evaluate_0.18 ps_1.7.2 fs_1.5.2 fansi_1.0.3
[45] nlme_3.1-160 xml2_1.3.3 tools_4.2.2 lifecycle_1.0.3
[49] stringr_1.5.0 Rhdf5lib_1.18.2 munsell_0.5.0 callr_3.7.3
[53] compiler_4.2.2 jquerylib_0.1.4 systemfonts_1.0.4 rlang_1.0.6
[57] grid_4.2.2 rhdf5filters_1.8.0 rstudioapi_0.14 rmarkdown_2.18
[61] gtable_0.3.1 DBI_1.1.3 R6_2.5.1 bit_4.0.5
[65] fastmap_1.1.0 utf8_1.2.2 rprojroot_2.0.3 stringi_1.7.8
[69] parallel_4.2.2 Rcpp_1.0.9 vctrs_0.5.1 tidyselect_1.2.0
[73] xfun_0.35