how to retrieve binding affinity matrix in diffbind

Question

[hamaor]

hey everyone, I'm performing ChIP-Seq analysis using diffbind, after doing:

dba.count(peaksets, summits=250)

I would like to get the binding affinity Matrix into a text file.

help will be highly appriciated!!

Answer 1

[Rory Stark]

dba.peakset(myDBA, bRetrieve=TRUE, writeFile="BindingAffinityMatrix.csv")

The values will be the score used in dba.count(), the default is DBA_SCORE_TMM_MINUS_FULL (TMM normalised read counts after subtracting control reads, based on the number of reads in each bam file). To get, for example, raw read counts, use DBA_SCORE_READS. See help page for dba.count(). You can change the score without recounting:

myDBA <- dba.count(myDBA, peaks=NULL, score=DBA_SCORE_xxx)

[black293t]

Hi Rory,

From the latest update, I cannot retrieve the data from dab.report output. The error message is:

res_deseq <- dba.report(a, method=DBA_DESEQ2, contrast = 1, th=1) Error in .Call2("C_solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 10: at least two out of 'start', 'end', and 'width', must be supplied.

Does it require a new argument? I'm using the latest R (v4.0) and it happened after all dependencies were updated.

Thanks,

Keita

[Rory Stark]

This issue should now be fixed in version DiffBind_3.0.6. You'll need to re-run the analysis from dba.analyze().

Answer 2

[iamjli]

For completeness, this question has been answered here.