Nothing
get_sc_signature <- function(targetobj, gs_test = gs_c2_exps, padjcutoff = 0.01, gsea_cutoff = 0.3,
negctrlgenelist = "NonTargetingControlGuideForHuman") {
# select_gs_names=grep('^KEGG|^BIOCARTA|^REACTOME|^PID',gs_c2$names,invert = T) padjcutoff=0.01
select_gs_names = gs_test$names
scalef = getscaledata(targetobj)
r_cs = matrix(rep(0, length(select_gs_names) * ncol(scalef)), nrow = length(select_gs_names))
rownames(r_cs) = select_gs_names
colnames(r_cs) = colnames(scalef)
for (gs_pw in 1:length(select_gs_names)) {
# search_ind=which(select_gs_names==gs_pw)
if (gs_pw%%10 == 1) {
message(paste(gs_pw, "/", length(select_gs_names)))
}
gs_target = gs_test$geneset[gs_pw]
gs_name = gs_test$names[gs_pw]
# message(gs_name) target_gene='MKI67'
texp_mat = scalef[rownames(scalef) %in% gs_target[[1]], ]
texp = colMeans(texp_mat)
r_cs[gs_pw, ] = texp
# texp=sort(texp)
}
return(r_cs)
}
TRUE
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