Question: Subsetting DESeq2 results by padj quantity
0
gravatar for rbronste
20 months ago by
rbronste260
rbronste260 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 • 976 views
ADD COMMENTlink modified 20 months ago by mbk0asis460 • written 20 months ago by rbronste260
3
gravatar for mbk0asis
20 months ago by
mbk0asis460
Korea, Republic Of
mbk0asis460 wrote:
dta <- subset(result, padj<.1)
dta_sorted = dta[order(dta$padj), ]
write.table(head(dta_sorted,1000),"dta.tsv")
ADD COMMENTlink modified 20 months ago • written 20 months ago by mbk0asis460

Exactly what I was after, thanks!

ADD REPLYlink written 20 months ago by rbronste260
0
gravatar for WouterDeCoster
20 months ago by
Belgium
WouterDeCoster40k wrote:

You could use the head() function

e.g.:

head(df, n=1000)
ADD COMMENTlink modified 20 months ago • written 20 months ago by WouterDeCoster40k

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 20 months ago • written 20 months ago by rbronste260

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

ADD REPLYlink written 20 months ago by WouterDeCoster40k
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