pianopiano 2.0.2
library(piano)## Registered S3 methods overwritten by 'ggplot2':
## method from
## [.quosures rlang
## c.quosures rlang
## print.element sets
## print.quosures rlangdata("gsa_input")head(gsa_input$gsc,10)## g s
## [1,] "g103" "s1"
## [2,] "g106" "s19"
## [3,] "g118" "s16"
## [4,] "g130" "s21"
## [5,] "g130" "s6"
## [6,] "g131" "s46"
## [7,] "g132" "s32"
## [8,] "g132" "s3"
## [9,] "g139" "s1"
## [10,] "g140" "s21"head(gsa_input$pvals, 10)## g1 g2 g3 g4 g5
## 2.351900e-05 2.838832e-05 2.885141e-05 6.566243e-05 7.107615e-05
## g6 g7 g8 g9 g10
## 7.770070e-05 1.436830e-04 1.532264e-04 1.626607e-04 1.644806e-04head(gsa_input$directions, 10)## g1 g2 g3 g4 g5 g6 g7 g8 g9 g10
## -1 -1 1 -1 -1 1 -1 -1 -1 -1geneSets <- loadGSC(gsa_input$gsc)
geneSets## First 50 (out of 50) gene set names:
## [1] "s1" "s19" "s16" "s21" "s6" "s46" "s32" "s3" "s34" "s14" "s7" "s13"
## [13] "s5" "s42" "s2" "s11" "s22" "s8" "s15" "s10" "s33" "s37" "s35" "s43"
## [25] "s36" "s27" "s17" "s9" "s23" "s30" "s18" "s25" "s41" "s24" "s20" "s39"
## [37] "s31" "s12" "s29" "s4" "s26" "s44" "s28" "s47" "s38" "s49" "s50" "s40"
## [49] "s45" "s48"
##
## First 50 (out of 1136) gene names:
## [1] "g103" "g139" "g150" "g235" "g304" "g479" "g130" "g157" "g171" "g180"
## [11] "g218" "g243" "g251" "g302" "g319" "g32" "g329" "g372" "g373" "g403"
## [21] "g41" "g43" "g456" "g476" "g48" "g521" "g527" "g554" "g581" "g585"
## [31] "g591" "g62" "g660" "g665" "g698" "g71" "g711" "g723" "g726" "g75"
## [41] "g758" "g77" "g808" "g816" "g838" "g9" "g907" "g924" "g931" "g935"
##
## Gene set size summary:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 2.00 20.50 39.00 39.50 53.75 95.00
##
## No additional info available.gsares <- runGSA(gsa_input$pvals,
gsa_input$directions,
gsc = geneSets,
nPerm = 500) # set to 500 for fast runNote: nPerm was set to 500 to get a short runtime for this vignette, in reality use a higher number, e.g. 10,000 (default).
exploreGSAres(gsares)This opens a browser window with an interactive interface where the results can be explored in detail.
Here is the output of sessionInfo() on the system on which this document was compiled.
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.9-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.9-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] piano_2.0.2 BiocStyle_2.12.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.1 lattice_0.20-38 visNetwork_2.0.6
## [4] relations_0.6-8 gtools_3.8.1 assertthat_0.2.1
## [7] digest_0.6.19 mime_0.6 slam_0.1-45
## [10] R6_2.4.0 plyr_1.8.4 evaluate_0.13
## [13] ggplot2_3.1.1 pillar_1.4.0 gplots_3.0.1.1
## [16] rlang_0.3.4 lazyeval_0.2.2 data.table_1.12.2
## [19] gdata_2.18.0 Matrix_1.2-17 DT_0.6
## [22] rmarkdown_1.12 sets_1.0-18 shinyjs_1.0
## [25] BiocParallel_1.18.0 stringr_1.4.0 htmlwidgets_1.3
## [28] igraph_1.2.4.1 munsell_0.5.0 shiny_1.3.2
## [31] fgsea_1.10.0 compiler_3.6.0 httpuv_1.5.1
## [34] xfun_0.7 pkgconfig_2.0.2 BiocGenerics_0.30.0
## [37] marray_1.62.0 htmltools_0.3.6 tidyselect_0.2.5
## [40] tibble_2.1.1 gridExtra_2.3 bookdown_0.10
## [43] crayon_1.3.4 dplyr_0.8.1 later_0.8.0
## [46] bitops_1.0-6 grid_3.6.0 jsonlite_1.6
## [49] xtable_1.8-4 gtable_0.3.0 magrittr_1.5
## [52] scales_1.0.0 KernSmooth_2.23-15 stringi_1.4.3
## [55] promises_1.0.1 limma_3.40.2 fastmatch_1.1-0
## [58] tools_3.6.0 Biobase_2.44.0 glue_1.3.1
## [61] purrr_0.3.2 parallel_3.6.0 yaml_2.2.0
## [64] colorspace_1.4-1 cluster_2.0.9 BiocManager_1.30.4
## [67] caTools_1.17.1.2 shinydashboard_0.7.1 knitr_1.23