DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
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@pierre-lindenbaum-6329
Last seen 11 days ago
France

Hi all,

I'm new to diffbind.

I've been given a set of ATAC-seq data computed with nf-core/atacseq and asked if there is any peak associated with the sex of the individuals.

In my samplesheet i set the following columns:

  • Tissue tissue1 || tissue2 || tissue3

  • Condition M || F # male of female

  • Factor NA

my workflow , copied from a former colleague's code, contains the following calls:

    dba(samplesheet)
    dba.count(DBA, bParallel=FALSE) ## my job used to be killed for dba.countby our cluster until I downsampled the bams
    dba.normalize(DBA)
    dba.contrast(DBANorm, categories = DBA_CONDITION)
    dba.analyze(DBAContrast, method=c(DBA_DESEQ2))
    dba.report(DNAAnalysis, th = 1, bCalled=TRUE, method=DBA_DESEQ2)

and then I save the file:

  df <- data.frame(CHROM=seqnames(DBA.report),
                   starts=start(DBA.report)-1,
                   ends=end(DBA.report),
                   names=c(paste0("peak",1:length(DBA.report))),
                   scores=c(rep("0", length(DBA.report))),
                   strands=c(rep(".", length(DBA.report))),
                   conc = DBA.report\$Conc,
                   conc_cond1=mcols(DBA.report)[,2],
                   conc_cond2=mcols(DBA.report)[,3],
                   fold = DBA.report\$Fold,
                   pval = DBA.report\$"p-value",
                   FDR = DBA.report\$FDR
                )

1) for dba.contrast, currently my phenotype is a binary one. In general is it ok if the column Condition contains more than two items (eg: brown eye, blue eye, gray eye).

2) what is group1 and group2 in my context ? male / female ? female / make ? how do i know the context ? is there a group3 if my phenotype is not binary ?

3) after dba.analyze I tried dba.plotVenn(DBA,contrast=1,method=DBA_DESEQ2) to plot a venn diagram of male vs female but it failed (I don't hae the error message anymore). Why ? I'm not sure about this . I don't really get the idea that dba.show returns contrasts associated with a DBA object. . So should I 'loop' over all the contrasts returned by dba.show ?

4) if I want to find the difference by cell-type AND sex I should use dba.contrast(DBA categories = c(DBA_CONDITION,Tissue))` right ?

5) unless I'm wrong, even If I use DBA <- dba.contrast(DBA , categories = DBA_TISSUE) I see Conc_F Conc_M in the DBA.report. Is the report only for "Condition" ?

> head(DBA.report)
GRanges object with 6 ranges and 8 metadata columns:
    seqnames        ranges strand |      Conc    Conc_F    Conc_M         Fold
       <Rle>     <IRanges>  <Rle> | <numeric> <numeric> <numeric>    <numeric>
  1     chr1    9915-10315      * |   6.61318   6.74846   6.49502  0.000946031
  2     chr1   13124-13524      * |   4.57819   4.32214   4.75464 -0.001598787
  3     chr1   17175-17575      * |   5.03964   5.39257   4.67800  0.004456263
  4     chr1   29117-29517      * |   6.12669   5.23852   6.57850 -0.004478228
  5     chr1 181182-181582      * |   6.91771   7.39266   6.37842  0.002882007
  6     chr1 183675-184075      * |   6.24583   6.55481   5.93992  0.002751221
`

6) if I'm interested in the peaks in the autosomal chromosomes associated to sex, should I remove the data in the sexual chromosome not remove any bias ?

Thank you for your help

Pierre

DiffBind ATACSeq • 68 views
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