pianopiano 2.23.0
library(piano)
data("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 g6
## 2.351900e-05 2.838832e-05 2.885141e-05 6.566243e-05 7.107615e-05 7.770070e-05
## g7 g8 g9 g10
## 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 Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] piano_2.23.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] fastmatch_1.1-4 gtable_0.3.6 xfun_0.48
## [4] bslib_0.8.0 ggplot2_3.5.1 visNetwork_2.1.2
## [7] shinyjs_2.1.0 htmlwidgets_1.6.4 sets_1.0-25
## [10] caTools_1.18.3 Biobase_2.67.0 lattice_0.22-6
## [13] vctrs_0.6.5 tools_4.5.0 bitops_1.0-9
## [16] generics_0.1.3 parallel_4.5.0 tibble_3.2.1
## [19] fansi_1.0.6 cluster_2.1.6 pkgconfig_2.0.3
## [22] Matrix_1.7-1 KernSmooth_2.23-24 data.table_1.16.2
## [25] lifecycle_1.0.4 compiler_4.5.0 gplots_3.2.0
## [28] statmod_1.5.0 munsell_0.5.1 fgsea_1.33.0
## [31] codetools_0.2-20 httpuv_1.6.15 htmltools_0.5.8.1
## [34] sass_0.4.9 yaml_2.3.10 marray_1.85.0
## [37] later_1.3.2 pillar_1.9.0 jquerylib_0.1.4
## [40] relations_0.6-13 DT_0.33 BiocParallel_1.41.0
## [43] cachem_1.1.0 limma_3.63.0 mime_0.12
## [46] gtools_3.9.5 tidyselect_1.2.1 digest_0.6.37
## [49] slam_0.1-54 dplyr_1.1.4 bookdown_0.41
## [52] cowplot_1.1.3 fastmap_1.2.0 grid_4.5.0
## [55] colorspace_2.1-1 cli_3.6.3 magrittr_2.0.3
## [58] utf8_1.2.4 scales_1.3.0 promises_1.3.0
## [61] rmarkdown_2.28 igraph_2.1.1 shiny_1.9.1
## [64] evaluate_1.0.1 knitr_1.48 rlang_1.1.4
## [67] Rcpp_1.0.13 xtable_1.8-4 glue_1.8.0
## [70] BiocManager_1.30.25 BiocGenerics_0.53.0 shinydashboard_0.7.2
## [73] jsonlite_1.8.9 R6_2.5.1