8 Final section
Record time and objects in the environment at the end of analysis:
Sys.time()## [1] "2020-04-08 16:25:51 BST"ls()## [1] "all_genes_intersect.df" "base_folder" "colorize" "ddx" "DEGs_intersect.df" "DESeq2_fc_2_fdr_0.01_all_genes.df" "DESeq2_fc_2_fdr_0.01_DEGs.df" "design" "dgl" "edgeR_fc2" "edgeR_fc2_all_genes" "edgeR_fc2_fdr_0.01" "fit" "genes.df" "samples.df" "vst_dds"sessionInfo()## R version 3.6.2 (2019-12-12)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.4
##
## 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_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] VennDiagram_1.6.20 futile.logger_1.4.3 edgeR_3.28.1 limma_3.42.2 DESeq2_1.26.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.2 BiocParallel_1.20.1 matrixStats_0.56.0 Biobase_2.46.0 rtracklayer_1.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.3 BiocGenerics_0.32.0 dplyr_0.8.5 knitr_1.28
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 tools_3.6.2 backports_1.1.6 R6_2.4.1 rpart_4.1-15 Hmisc_4.4-0 DBI_1.1.0 colorspace_1.4-1 nnet_7.3-13 tidyselect_1.0.0 gridExtra_2.3 bit_1.1-15.2 compiler_3.6.2 cli_2.0.2 formatR_1.7 htmlTable_1.13.3 labeling_0.3 bookdown_0.18 scales_1.1.0 checkmate_2.0.0 genefilter_1.68.0 stringr_1.4.0 digest_0.6.25 Rsamtools_2.2.3 foreign_0.8-76 rmarkdown_2.1 XVector_0.26.0 base64enc_0.1-3 jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.4.0 htmlwidgets_1.5.1 rlang_0.4.5 rstudioapi_0.11 RSQLite_2.2.0 farver_2.0.3 acepack_1.4.1
## [40] RCurl_1.98-1.1 magrittr_1.5 GenomeInfoDbData_1.2.2 Formula_1.2-3 Matrix_1.2-18 Rcpp_1.0.4 munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0 stringi_1.4.6 yaml_2.2.1 zlibbioc_1.32.0 blob_1.2.1 crayon_1.3.4 lattice_0.20-41 Biostrings_2.54.0 splines_3.6.2 annotate_1.64.0 locfit_1.5-9.4 pillar_1.4.3 geneplotter_1.64.0 futile.options_1.0.1 XML_3.99-0.3 glue_1.4.0 evaluate_0.14 latticeExtra_0.6-29 lambda.r_1.2.4 data.table_1.12.8 png_0.1-7 vctrs_0.2.4 gtable_0.3.0 purrr_0.3.3 assertthat_0.2.1 ggplot2_3.3.0 xfun_0.12 xtable_1.8-4 survival_3.1-11 tibble_3.0.0 GenomicAlignments_1.22.1
## [79] AnnotationDbi_1.48.0 memoise_1.1.0 cluster_2.1.0 ellipsis_0.3.0