Code for Primary Immune Deficiency (PID) analysis presented in Thaventhiran et al. This code is for illustrative purposes only and will not run without necessary resource files.
R version 3.3.3 (2017-03-06)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux 7.5 (Nitrogen)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=en_GB.UTF-8
[9] LC_ADDRESS=en_GB.UTF-8 LC_TELEPHONE=en_GB.UTF-8
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=en_GB.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] xlsx_0.5.7 xlsxjars_0.6.1
[3] rJava_0.9-9 wgsea_1.8
[5] snpStats_1.24.0 Matrix_1.2-8
[7] survival_2.41-3 simGWAS_0.1-0
[9] rtracklayer_1.32.2 reshape2_1.4.3
[11] RColorBrewer_1.1-2 rCOGS_0.0.0.9000
[13] optparse_1.4.4 Gviz_1.18.2
[15] ggrepel_0.7.0 GenomicInteractions_1.8.1
[17] InteractionSet_1.2.1 SummarizedExperiment_1.4.0
[19] Biobase_2.34.0 GenomicRanges_1.26.4
[21] GenomeInfoDb_1.10.3 IRanges_2.8.2
[23] S4Vectors_0.12.2 BiocGenerics_0.20.0
[25] cowplot_0.9.2 ggplot2_2.2.1
[27] biomaRt_2.30.0 magrittr_1.5
[29] devtools_1.13.5 data.table_1.11.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.53.1
[3] bit64_0.9-7 httr_1.3.1
[5] tools_3.3.3 backports_1.1.2
[7] R6_2.2.2 rpart_4.1-10
[9] Hmisc_4.1-1 DBI_1.0.0
[11] lazyeval_0.2.1 colorspace_1.3-2
[13] nnet_7.3-12 withr_2.1.1
[15] gridExtra_2.3 bit_1.1-12
[17] htmlTable_1.11.2 scales_0.5.0
[19] checkmate_1.8.5 mvtnorm_1.0-7
[21] stringr_1.3.1 digest_0.6.15
[23] Rsamtools_1.26.2 foreign_0.8-69
[25] XVector_0.14.1 base64enc_0.1-3
[27] dichromat_2.0-0 pkgconfig_2.0.1
[29] htmltools_0.3.6 ensembldb_1.6.2
[31] BSgenome_1.42.0 htmlwidgets_1.0
[33] rlang_0.2.0 rstudioapi_0.7
[35] RSQLite_2.1.1 BiocInstaller_1.24.0
[37] shiny_1.0.5 bindr_0.1
[39] combinat_0.0-8 BiocParallel_1.8.2
[41] acepack_1.4.1 dplyr_0.7.4
[43] VariantAnnotation_1.20.3 RCurl_1.95-4.10
[45] Formula_1.2-2 Rcpp_0.12.16
[47] munsell_0.4.3 stringi_1.2.4
[49] yaml_2.2.0 zlibbioc_1.20.0
[51] plyr_1.8.4 AnnotationHub_2.6.5
[53] blob_1.1.1 lattice_0.20-34
[55] Biostrings_2.42.1 splines_3.3.3
[57] GenomicFeatures_1.26.4 knitr_1.20
[59] pillar_1.2.1 igraph_1.1.2
[61] corpcor_1.6.9 XML_3.98-1.11
[63] glue_1.2.0 biovizBase_1.22.0
[65] latticeExtra_0.6-28 httpuv_1.3.6.2
[67] getopt_1.20.2 gtable_0.2.0
[69] assertthat_0.2.0 mime_0.5
[71] xtable_1.8-2 tibble_1.4.2
[73] GenomicAlignments_1.10.1 AnnotationDbi_1.36.2
[75] memoise_1.1.0 bindrcpp_0.2
[77] cluster_2.0.6 interactiveDisplayBase_1.12.0