library("DiffBind")

siDDX5 <-dba(sampleSheet="siDDX5.csv")

siDDX5 <- dba.count(summits=FALSE,siDDX5, bUseSummarizeOverlaps=TRUE)

siDDX5 <- dba.contrast(siDDX5, categories=DBA_TREATMENT,minMembers =2)

siDDX5 <- dba.analyze(siDDX5, method=DBA_ALL_METHODS)

comp1.deseq <- dba.report(siDDX5, method=DBA_DESEQ2, contrast = 1,
th=1)

out <- as.data.frame(comp1.deseq) deseq.bed <- out[ which(out$FDR < 0.1),
c("seqnames", "start", "end", "strand", "Fold")]
write.table(deseq.bed,file="results/siDDX5/siDDX5_vs_control_deseq2_sig.bed", sep="t", quote=F, row.names=F, col.names=F)

Analyzing...

Adding contrasts(s)...

Analyze error: Error in pv.DBA(DBA, method, bTagwise = bTagwise,
minMembers = 3, bParallel = bParallel): Unable to perform analysis: no
contrasts specified.

siDDX5

4 Samples, 43921 sites in matrix (87804 total):

ID Treatment Replicate Intervals

1 Control1 Control 1 42372

2 Control2 Control 2 50406

3 siDDX5-1 siDDX5 1 66390

4 siDDX5-2 siDDX5 2 61316



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