ChIP peak data set comparison

Question

[s.singh]

Hi all,

I am fairly new to coding and am trying to work through the ChIPSeeker package using my own data in R. I am not sure how to input multiple files (.bed) into the getTagMatrix command. I want to generate profiles of ChIP peaks among different experiments. I want to compare ChIP peaks of two different experiment.

Can someone give me any advice?

Thanks Swadha

Answer 1

[pariksheet.nanda]

Read in the .bed files using the import.bed() function of the rtracklayer bioconductor package. import.bed() returns a GRanges object which getTagMatrix() accepts.