piano
piano 2.18.0
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-04
head(gsa_input$directions, 10)
## g1 g2 g3 g4 g5 g6 g7 g8 g9 g10
## -1 -1 1 -1 -1 1 -1 -1 -1 -1
geneSets <- loadGSC(gsa_input$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 run
Note: 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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_2.18.0 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] fastmatch_1.1-4 gtable_0.3.4 xfun_0.40
## [4] bslib_0.5.1 ggplot2_3.4.4 visNetwork_2.1.2
## [7] shinyjs_2.1.0 htmlwidgets_1.6.2 sets_1.0-24
## [10] caTools_1.18.2 Biobase_2.62.0 lattice_0.22-5
## [13] vctrs_0.6.4 tools_4.3.1 bitops_1.0-7
## [16] generics_0.1.3 parallel_4.3.1 tibble_3.2.1
## [19] fansi_1.0.5 cluster_2.1.4 pkgconfig_2.0.3
## [22] Matrix_1.6-1.1 KernSmooth_2.23-22 data.table_1.14.8
## [25] lifecycle_1.0.3 compiler_4.3.1 gplots_3.1.3
## [28] statmod_1.5.0 munsell_0.5.0 fgsea_1.28.0
## [31] codetools_0.2-19 httpuv_1.6.12 htmltools_0.5.6.1
## [34] sass_0.4.7 yaml_2.3.7 marray_1.80.0
## [37] later_1.3.1 pillar_1.9.0 jquerylib_0.1.4
## [40] ellipsis_0.3.2 relations_0.6-13 DT_0.30
## [43] BiocParallel_1.36.0 cachem_1.0.8 limma_3.58.0
## [46] mime_0.12 gtools_3.9.4 tidyselect_1.2.0
## [49] digest_0.6.33 slam_0.1-50 dplyr_1.1.3
## [52] bookdown_0.36 cowplot_1.1.1 fastmap_1.1.1
## [55] grid_4.3.1 colorspace_2.1-0 cli_3.6.1
## [58] magrittr_2.0.3 utf8_1.2.4 scales_1.2.1
## [61] promises_1.2.1 rmarkdown_2.25 igraph_1.5.1
## [64] shiny_1.7.5.1 evaluate_0.22 knitr_1.44
## [67] rlang_1.1.1 Rcpp_1.0.11 xtable_1.8-4
## [70] glue_1.6.2 BiocManager_1.30.22 BiocGenerics_0.48.0
## [73] shinydashboard_0.7.2 jsonlite_1.8.7 R6_2.5.1