Last updated: 2023-01-11
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Unstaged changes:
Modified: analysis/index_5.batches.Rmd
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| Neogen_Sample_ID | Missing | AA | AC | AG | AT | CC | CG | GC | GG | TA | TC | TG | TT | Total_Genotyped | Percent_Genotyped | MURGIGV01_SNP.Count | cr |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NM00185-ICI-Myo | 5321 | 30457 | 1344 | 5697 | 9 | 31614 | 9 | 3 | 31761 | 2 | 5473 | 1348 | 30221 | 137938 | 96.29% | 143259 | 0.962857481903406 |
| D38-ICI-Myo | 5346 | 29342 | 1811 | 7276 | 6 | 30520 | 6 | 4 | 30855 | 3 | 7190 | 1758 | 29142 | 137913 | 96.27% | 143259 | 0.962682972797521 |
| 7927-ICI-Myo | 5635 | 29819 | 1580 | 6562 | 8 | 30883 | 2 | 4 | 31138 | 3 | 6327 | 1566 | 29732 | 137624 | 96.07% | 143259 | 0.960665647533488 |
| D517-ICI-Myo | 5197 | 28387 | 2202 | 9091 | 8 | 29402 | 5 | 5 | 29675 | 4 | 8944 | 2130 | 28209 | 138062 | 96.37% | 143259 | 0.963723047068596 |
| D1-PBS-Myo | 5788 | 29470 | 1696 | 7014 | 7 | 30635 | 6 | 7 | 30856 | 1 | 6917 | 1689 | 29173 | 137471 | 95.96% | 143259 | 0.959597651805471 |
| D40-ICI-Myo | 5330 | 29364 | 1789 | 7341 | 10 | 30473 | 5 | 3 | 30797 | 0 | 7342 | 1735 | 29070 | 137929 | 96.28% | 143259 | 0.962794658625287 |
| D251-PBS-Myo | 5465 | 29931 | 1566 | 6519 | 7 | 30923 | 8 | 5 | 31165 | 1 | 6475 | 1571 | 29623 | 137794 | 96.19% | 143259 | 0.961852309453507 |
| D344-ICI-Myo | 5362 | 30055 | 1556 | 6501 | 7 | 30944 | 8 | 4 | 31168 | 3 | 6330 | 1520 | 29801 | 137897 | 96.26% | 143259 | 0.962571286969754 |
| D90-ICI-EOI | 5445 | 28203 | 2173 | 9129 | 7 | 29457 | 7 | 4 | 29735 | 3 | 8895 | 2061 | 28140 | 137814 | 96.20% | 143259 | 0.961991916738215 |
| 6874-PBS-Myo | 5336 | 29392 | 1818 | 7305 | 6 | 30462 | 7 | 4 | 30783 | 4 | 7126 | 1718 | 29298 | 137923 | 96.28% | 143259 | 0.962752776439875 |
| D351-ICI-Myo | 21879 | 25617 | 1613 | 6385 | 4 | 27012 | 5 | 6 | 27387 | 2 | 6222 | 1581 | 25546 | 121380 | 84.73% | 143259 | 0.847276610893556 |
| 7168-ICI-Myo | 5555 | 31493 | 968 | 3897 | 6 | 32509 | 7 | 4 | 32790 | 0 | 3787 | 968 | 31275 | 137704 | 96.12% | 143259 | 0.961224076672321 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| NM00185-ICI-Myo | F | F |
| D38-ICI-Myo | F | M |
| 7927-ICI-Myo | F | F |
| D517-ICI-Myo | F | F |
| D1-PBS-Myo | F | F |
| D40-ICI-Myo | F | F |
| D251-PBS-Myo | F | F |
| D344-ICI-Myo | F | F |
| D90-ICI-EOI | M | M |
| 6874-PBS-Myo | F | F |
| D351-ICI-Myo | F | M |
| 7168-ICI-Myo | F | F |
| Neogen_Sample_ID | Myocarditis.Status | age.of.clinical.phenotype..weeks. | clinical.pheno | Drug.Treatment |
|---|---|---|---|---|
| NM00185-ICI-Myo | YES | 13.1 | SICK | ICI |
| D38-ICI-Myo | YES | 17.9 | SICK | ICI |
| 7927-ICI-Myo | YES | 13.3 | SICK | ICI |
| D517-ICI-Myo | YES | 13 | SICK | ICI |
| D1-PBS-Myo | YES | 38.3 | SICK | PBS |
| D40-ICI-Myo | YES | 12.9 | SICK | ICI |
| D251-PBS-Myo | YES | 12.3 | SICK | PBS |
| D344-ICI-Myo | YES | 13 | SICK | ICI |
| D90-ICI-EOI | NO | – | EOI | ICI |
| 6874-PBS-Myo | YES | 21.1 | SICK | PBS |
| D351-ICI-Myo | YES | 13 | SICK | ICI |
| 7168-ICI-Myo | YES | 13.3 | SICK | ICI |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex | |
|---|---|---|---|---|
| 2 | D38-ICI-Myo | XX | ||
| 11 | D351-ICI-Myo | XX | XX |
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] tibble_3.1.8 readxl_1.4.1 cluster_2.1.4 dplyr_1.0.10
[5] optparse_1.7.3 rhdf5_2.40.0 mclust_6.0.0 tidyr_1.2.1
[9] data.table_1.14.6 knitr_1.41 kableExtra_1.3.4 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.35 bslib_0.4.1 purrr_0.3.5
[5] colorspace_2.0-3 vctrs_0.5.1 generics_0.1.3 getopt_1.20.3
[9] htmltools_0.5.3 viridisLite_0.4.1 yaml_2.3.6 utf8_1.2.2
[13] rlang_1.0.6 jquerylib_0.1.4 later_1.3.0 pillar_1.8.1
[17] withr_2.5.0 DBI_1.1.3 glue_1.6.2 lifecycle_1.0.3
[21] stringr_1.5.0 cellranger_1.1.0 munsell_0.5.0 rvest_1.0.3
[25] evaluate_0.18 callr_3.7.3 fastmap_1.1.0 httpuv_1.6.6
[29] ps_1.7.2 fansi_1.0.3 Rcpp_1.0.9 promises_1.2.0.1
[33] scales_1.2.1 cachem_1.0.6 webshot_0.5.4 jsonlite_1.8.4
[37] fs_1.5.2 systemfonts_1.0.4 digest_0.6.30 stringi_1.7.8
[41] processx_3.8.0 getPass_0.2-2 rprojroot_2.0.3 rhdf5filters_1.8.0
[45] cli_3.4.1 tools_4.2.2 magrittr_2.0.3 sass_0.4.4
[49] whisker_0.4.1 pkgconfig_2.0.3 ellipsis_0.3.2 xml2_1.3.3
[53] assertthat_0.2.1 rmarkdown_2.18 svglite_2.1.0 httr_1.4.4
[57] rstudioapi_0.14 Rhdf5lib_1.18.2 R6_2.5.1 git2r_0.30.1
[61] compiler_4.2.2