Export data from R
export(object, con, ...) # S4 method for FgseaList,character export( object, con, geneSetResults = FALSE, compress = FALSE, overwrite = TRUE, quiet = FALSE )
character(1). Directory path.
character. Export per-gene set expression including log fold change values generated from DESeq2. Can be slow when processing all MSigDB collections, so disabled by default. Alternatively, can declare specific collections to process (see
collectionNamesfor supported values).
logical(1). Apply gzip compression to all files.
logical(1). Overwrite existing file on disk.
logical(1). Perform command quietly, suppressing messages.
file.path("object", "mutant_vs_control", "c1.csv")
S4 object is currently structured by:
Gene set (c1-c8, h).
The object was structured in this manner to flow with the R Markdown template. However, when writing to disk, I think it makes more sense to organize by:
data(fgsea) ## FgseaList ==== object <- fgsea con <- AcidBase::tempdir2() out <- export( object = object, con = con ) #> → Exporting <FgseaList> to '/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9TkQ9s/BvCptbuYW2-169644920193096'. #> → Exporting results for `condition_B_vs_A`. #> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9TkQ9s/BvCptbuYW2-169644920193096/condition_B_vs_A/h_all_v7_0_symbols.csv using base::`write.table()`. #> → Exporting results for `treatment_D_vs_C`. #> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9TkQ9s/BvCptbuYW2-169644920193096/treatment_D_vs_C/h_all_v7_0_symbols.csv using base::`write.table()`. print(out) #> $condition_B_vs_A #> $condition_B_vs_A$h_all_v7_0_symbols #>  "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9TkQ9s/BvCptbuYW2-169644920193096/condition_B_vs_A/h_all_v7_0_symbols.csv" #> #> #> $treatment_D_vs_C #> $treatment_D_vs_C$h_all_v7_0_symbols #>  "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9TkQ9s/BvCptbuYW2-169644920193096/treatment_D_vs_C/h_all_v7_0_symbols.csv" #> #> AcidBase::unlink2(con)