vignettes/gsea.Rmd
gsea.RmdShould use SE transcriptomics dataset instead?
#library(ariadne)
#library(GEOquery)
#eList <- getGEO("GSE11675")
#eData <- eList[[1]]
#eData
#head(exprs(eData))
#genes <- featureData(eData)@data$ENTREZ_GENE_ID
#head(genes)
#graph <- ariadne()
#plotPath(graph, geneid ~ msig, prune = TRUE, focus = TRUE)
#gene2msig <- weavePath(graph, geneid ~ msig, init = genes)
#head(gene2msig)R session information:
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.39 desc_1.4.3 R6_2.6.1 bookdown_0.47 fastmap_1.2.0
## [6] xfun_0.59 cachem_1.1.0 knitr_1.51 htmltools_0.5.9 rmarkdown_2.31
## [11] lifecycle_1.0.5 cli_3.6.6 sass_0.4.10 pkgdown_2.2.1 textshaping_1.0.5
## [16] jquerylib_0.1.4 systemfonts_1.3.2 compiler_4.6.1 tools_4.6.1 ragg_1.5.2
## [21] bslib_0.11.0 evaluate_1.0.5 yaml_2.3.12 BiocManager_1.30.27 otel_0.2.0
## [26] jsonlite_2.0.0 rlang_1.3.0 fs_2.1.0 htmlwidgets_1.6.4