biobenkj/atacseeker

ATACseq tools for Bioconductor

atacseeker's Issues

help with generating `RangedSummarizedExperiment` for `compartmap::getATACABsignal` function

@biobenkj you seem to be the main developer for both compartmap and this ATACseeker R packages. I can see you are working with trichelab, as suggested by several forks, but it's hard to trace down which branch/fork is the most up to date. I've been using yours.

The ultimate aim for me is to call A/B compartment from ATACseq data and later annotate Hi-C with that information.

I've been hitting several issues with both compartmap and ATACseeker. Firstly compartmap::getCompartments() function doesn't exist and I was struggling to find traces of that function in the commits. I figured the function that I need to use is compartmap::getATACABsignal()

That function needs a RangedSummarizedExperiment object and this is the one I'm having lots of trouble generating. There is no documentation on how to make such object with ATACseeker. Specifically how did you make this object?

> data(bulkATAC_raw_filtered_chr14, package = "compartmap")
> filtered.data.chr14
class: RangedSummarizedExperiment 
dim: 11324 126 
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames(11324): 14_20443001-20443150 14_20443051-20443200 ... 14_107281251-107281400
  14_107281301-107281450
rowData names(0):
colnames(126): BulkCTCL_Patient11_Romi_Day0 BulkCTCL_Patient11_Romi_Day14 ...
  Normal_Donor7_Day38 Normal_Donor9_Day38
colData names(4): bam.files totals ext rlen

I have bam files and narrow peaks called with MACS2. narrow peaks file looks like this

track type=narrowPeak visibility=3 db=mm10 name="Sample A" description="Sample A - MACS2"
chr1    4496165 4496901 sampleA_1 783     .       15.65060        80.86877        78.32123        312
chr1    4747719 4748710 sampleA_2 508     .       13.48518        53.27889        50.85302        616
chr1    4768356 4768679 sampleA_3 306     .       9.96556 33.00044        30.69566        163
chr1    4769950 4770363 sampleA_4 189     .       7.42956 21.15988        18.95548        61
chr1    4779287 4779485 sampleA_5 59      .       4.00563 8.00378 5.98218 134

Any help will be much appreciated, Thanks !