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.

Thanks!

Do you know what Pearson correlation is? It measures the collinearity between two one dimensional measures.

I am only vaguely familiar with the test. I've seen it on a large amount of papers recently while reading up on a new project. Essentially what I am trying to do as quoted from a paper is "find the number of uniquely aligned reads per Pol II gene for two complete biological replicates generated from * insert cell type * cells (Pearson's correlation, R = 0.##)

There's no test. There's no hypothesis, and there's no p-value. The correlation is just a measurement.

You can window the data along the genome and calculate a correlation for the values in each window, but you definitely want to filter low windows. This post had some additional ideas.