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Rollup before configuration integration

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This commit is contained in:
Bryan Roessler
2024-08-17 15:24:04 -04:00
parent d1380f9c3b
commit 46f1e4d4d4
6034 changed files with 60 additions and 87 deletions
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18
workflow/apps/r/joinInteractExps.R
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@@ -42,12 +42,12 @@ for (i in seq_along(studies)) {
}
rm(zs_file, study)
for (var in ls()) {
print(paste(var, ":", get(var)))
}
# for (var in ls()) {
# print(paste(var, ":", get(var)))
# }
print(input_files)
print(length(input_files))
# print(input_files)
# print(length(input_files))
# TODO this is better handled in a loop in case you want to compare more experiments?
# The input is already designed for this
@@ -88,10 +88,10 @@ if (length(input_files) >= 4) {
headSel2 <- select(headSel2, -"Gene.1", -"Gene.2", -"Gene.3")
}
print(headers)
# print(headers)
# headSel$contains("Z_Shift") %>% replace_na(0.001)
headers <- colnames(headSel)
print(headers)
# print(headers)
i <- 0
for (i in 1:length(headers)) {
if (grepl("Shift", headers[i])) {
@@ -229,10 +229,10 @@ if (sd == 0) {
# write.csv(combI,file.path(out_dir,"CombinedKLzscores.csv"), row.names = FALSE)
write.csv(REMcRdy, file.path(out_dir, "REMcRdy_lm_only.csv"), row.names = FALSE, quote = FALSE)
write.csv(shiftOnly, file.path(out_dir, "Shift_only.csv"), row.names = FALSE, quote = FALSE)
#LabelStd <- read.table(file="./parameters.csv",stringsAsFactors = FALSE,sep = ",")
# LabelStd <- read.table(file="./parameters.csv",stringsAsFactors = FALSE,sep = ",")
LabelStd <- read.csv(file = study_info, stringsAsFactors = FALSE)
print(sd)
# print(sd)
LabelStd[, 4] <- as.numeric(sd)
write.csv(LabelStd, file = file.path(out_dir, "parameters.csv"), row.names = FALSE)
write.csv(LabelStd, file = study_info, row.names = FALSE)