Sum of allelic counts
for all autosomes, per sample
Allelic ratio per
chromosome
- Samples do not lie on the diagonal i.e. PWD counts are in general
lower than the FVB ones. This could be due to better annotation of FVB
SNPs than PWD ones.
- No experimental groups with a particularly high number of outliers,
which are potential anaeuploidic embryos.
- Outliers (bA10, bA12, bC4, bC19, bD20, bA11, bD5) will be excluded
from the rest of the analyses.
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dplyr_1.0.10 ggrepel_0.9.2 pheatmap_1.0.12 gridExtra_2.3
## [5] ggpubr_0.5.0 data.table_1.14.6 reshape2_1.4.4 ggplot2_3.4.0
##
## loaded via a namespace (and not attached):
## [1] prettydoc_0.4.1 tidyselect_1.2.0 xfun_0.35 bslib_0.4.1
## [5] purrr_0.3.5 carData_3.0-5 colorspace_2.0-3 vctrs_0.5.1
## [9] generics_0.1.3 htmltools_0.5.3 yaml_2.3.6 utf8_1.2.2
## [13] rlang_1.0.6 jquerylib_0.1.4 pillar_1.8.1 glue_1.6.2
## [17] withr_2.5.0 DBI_1.1.3 RColorBrewer_1.1-3 lifecycle_1.0.3
## [21] plyr_1.8.8 stringr_1.4.1 munsell_0.5.0 ggsignif_0.6.4
## [25] gtable_0.3.1 codetools_0.2-18 evaluate_0.18 labeling_0.4.2
## [29] knitr_1.40 fastmap_1.1.0 fansi_1.0.3 highr_0.9
## [33] broom_1.0.1 Rcpp_1.0.9 scales_1.2.1 backports_1.4.1
## [37] cachem_1.0.6 jsonlite_1.8.3 abind_1.4-5 farver_2.1.1
## [41] digest_0.6.30 stringi_1.7.8 rstatix_0.7.1 grid_4.1.3
## [45] cli_3.4.1 tools_4.1.3 magrittr_2.0.3 sass_0.4.2
## [49] tibble_3.1.8 tidyr_1.2.1 car_3.1-1 pkgconfig_2.0.3
## [53] assertthat_0.2.1 rmarkdown_2.18 rstudioapi_0.14 R6_2.5.1
## [57] compiler_4.1.3