Question: Meaning of columns in Chicdiff::chicdiffPipeline() output *_results.Rmd
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gravatar for adrija.kalvisa
13 months ago by
adrija.kalvisa0 wrote:

What is the content of Chicdiff::chicdiffPipeline() output from *_results.Rmd? I am currently following a tutorial on differential interaction calling (https://github.com/RegulatoryGenomicsGroup/chicdiff) and The column names of this output are the following:

[1] group
[2] baseMean
[3] log2FoldChange
[4] lfcSE
[5] stat
[6] pvalue
[7] padj
[8] baitID
[9] maxOE
[10] minOE
[11] regionID
[12] OEchr
[13] OEstart
[14] OEend
[15] baitchr
[16] baitstart
[17] baitend
[18] avDist
[19] uniform
[20] shuff
[21] avgLogDist
[22] avWeights
[23] weight
[24] weighted_pvalue
[25] weighted_padj

I assume that:
- columns 2-7 are from DESeq2 output.
- columns 8-17 describe bait and other end coordinates/IDs

However, I have trouble guessing what do column 1 and columns 18-25 mean. It looks like groups in column 1 are divided, based on 'avDist', and I guess the columns 18-25 has to do with how the p values are adjusted, taking into account the distance, but is there any more descriptive description of these columns?

R chicdiff capture hi-c pchi-c • 196 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 13 months ago by adrija.kalvisa0
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