I was wondering how to run a pearson correlation test between two chip-seq data sets. I have narrowpeak files for both which are essentially bed files.
Is there any bioconductor packages in R that can do this? I've tried a variety of bedtools, and programs such as CHANCE, but they haven't given me what I required.
I used MACS2 to call peaks.
I used Bowtie to align to hg19.