Commit d97dfb21 authored by Brandi Cantarel's avatar Brandi Cantarel

Merge branch 'dea.RFix' into 'master'

Corrected issue where a gene with 0 read counts could crash the dea.R scripts.

See merge request !3
parents 2adff316 18c034ed
Pipeline #2045 failed with stage
in 138 minutes and 6 seconds
process.executor='slurm'
process.queue='128GB,256GB,256GBv1'
process.clusterOptions = '--hold'
trace.enabled = true
trace.enabled = false
trace.file = 'pipeline_trace.txt'
trace.field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
Subproject commit 0bdf56d5bdb9252ce418fcf7d0c7bdbcee9ff4a1
Subproject commit 291e1c352873ce14881ab8b1822fa7d3183b946b
......@@ -94,6 +94,7 @@ for (i in 1:a) {
filt.out <- na.omit(output[output$fdr < 0.05,])
if (nrow(filt.out) > 2) {
subset <- logcpm[row.names(logcpm) %in% filt.out$symbol,]
subset <- subset[!apply(subset, 1, function(x) {any(x == 0)}),]
gnames <- filt.out[c('ensembl','symbol')]
s <- merge(gnames,subset,by.x="ensembl",by.y="row.names",all.x=FALSE,all.y=TRUE,sort=FALSE)
STREE <- hclust(dist(t(subset)))
......@@ -148,6 +149,7 @@ for (i in 1:a) {
filt.out <- na.omit(output[output$fdr < 0.05,])
if (nrow(filt.out) > 2) {
subset <- logcpm[row.names(logcpm) %in% filt.out$symbol,]
subset <- subset[!apply(subset, 1, function(x) {any(x == 0)}),]
gnames <- filt.out[c('ensembl','symbol')]
s <- merge(gnames,subset,by.x="ensembl",by.y="row.names",all.x=FALSE,all.y=TRUE,sort=FALSE)
STREE <- hclust(dist(t(subset)))
......
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