Question: Subsetting DESeq2 results by padj quantity
0
gravatar for rbronste
21 days ago by
rbronste150
rbronste150 wrote:

I am trying to export DESeq2 results that fall under a certain padj in the following way:

resFemEB<-results(dds, lfcThreshold=2, altHypothesis="greater", alpha = .1, format = c("GRanges"), independentFiltering=FALSE, contrast=c(1, -1/3, -1/3, -1/3))

resOrderedFemEB <- resFemEB[which(resFemEB$padj < 0.1),]

 df <- data.frame(seqnames=seqnames(resOrderedFemEB),
+                  starts=start(resOrderedFemEB)-1,
+                  ends=end(resOrderedFemEB),
+                  names=c(rep(".", length(resOrderedFemEB))),
+                  scores=c(rep(".", length(resOrderedFemEB))),
+                  strands=strand(resOrderedFemEB))
> write.table(df, file="resOrderedFemEB.bed", quote=F, sep="\t", row.names=F, col.names=F)

This works well for getting all of the results in a BED format that fall below a certain padj, what I wanted to ask is how I can just get the top 1000 exported (currently the list is around 10K that falls within that padj criteria)?

deseq deseq2 R • 201 views
ADD COMMENTlink modified 21 days ago by mbk0asis290 • written 21 days ago by rbronste150
3
gravatar for mbk0asis
21 days ago by
mbk0asis290
Korea, Republic Of
mbk0asis290 wrote:
dta <- subset(result, padj<.1)
dta_sorted = dta[order(dta$padj), ]
write.table(head(dta_sorted,1000),"dta.tsv")
ADD COMMENTlink modified 21 days ago • written 21 days ago by mbk0asis290

Exactly what I was after, thanks!

ADD REPLYlink written 20 days ago by rbronste150
0
gravatar for WouterDeCoster
21 days ago by
Belgium
WouterDeCoster24k wrote:

You could use the head() function

e.g.:

head(df, n=1000)
ADD COMMENTlink modified 21 days ago • written 21 days ago by WouterDeCoster24k

Thanks, yes this I know how to do, what I need is to export the top 1000 that fall under padj<.1, doing this currently to export them all:

write.table(df, file="resOrderedFemEB.bed", quote=F, sep="\t", row.names=F, col.names=F)
ADD REPLYlink modified 21 days ago • written 21 days ago by rbronste150

So then you need to sort the data frame based on padj and then take the head()

ADD REPLYlink written 21 days ago by WouterDeCoster24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 820 users visited in the last hour