Question: Subsetting DESeq2 results by padj quantity
0
gravatar for rbronste
14 months ago by
rbronste230
rbronste230 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 • 800 views
ADD COMMENTlink modified 14 months ago by mbk0asis410 • written 14 months ago by rbronste230
3
gravatar for mbk0asis
14 months ago by
mbk0asis410
Korea, Republic Of
mbk0asis410 wrote:
dta <- subset(result, padj<.1)
dta_sorted = dta[order(dta$padj), ]
write.table(head(dta_sorted,1000),"dta.tsv")
ADD COMMENTlink modified 14 months ago • written 14 months ago by mbk0asis410

Exactly what I was after, thanks!

ADD REPLYlink written 14 months ago by rbronste230
0
gravatar for WouterDeCoster
14 months ago by
Belgium
WouterDeCoster37k wrote:

You could use the head() function

e.g.:

head(df, n=1000)
ADD COMMENTlink modified 14 months ago • written 14 months ago by WouterDeCoster37k

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 14 months ago • written 14 months ago by rbronste230

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

ADD REPLYlink written 14 months ago by WouterDeCoster37k
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