Retrieving count averages from a binding matrix
I am interested in being able to retrieve count averages from a diffBind count matrix using a set of intervals, specifically to be able to limit my count average retrieval to specific columns in the count matrix of a set of unique intervals. Wondering if there are any good approaches to do that, thanks.
So the count matrix looks as follows:
MBV1 MBV2 MBV3 FBV1 FBV2 FBV3 MBE7 MBE8 MBE9 FBE1 FBE2 FBE3
4 1 1 1 1 1 1 1 66 1 1 50 34
5 22 1 1 1 1 1 6 98 1 22 100 1
And here is the DESeq2 results output example of a few rows:
log2 fold change (MLE): group EB vs vehicle
Wald test p-value: group EB vs vehicle
DataFrame with 324899 rows and 6 columns
baseMean log2FoldChange
4 chr1 3011001-3011351 * | 37.5265278603838 -0.245442215042177
5 chr1 3012575-3012925 * | 82.6779411160294 0.494119517305561
So I would like to take rows 4 and 5 that I got in the DESeq2 results and query count averages back in the matrix in specific columns, and to do this on many sites at once giving an input that has both the original row numbers as well as the GRanges of the final result.
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Ok so the count matrix looks as follows:
And here is the DESeq2 results output example of a few rows:
So I would like to take rows 4 and 5 that I got in the DESeq2 results and query count averages back in the matrix in specific columns, and to do this on many sites at once giving an input that has both the original row numbers as well as the GRanges of the final result.