How to use ChIPseeker to annotate peak

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ChIPseeker is one of the most widely used peak annotation software, providing the following functions

Visualization of peak distribution near chromosomes and TSS loci

Annotation of peak-associated genes and their distribution on various elements of the genome

Get the bed file of peak in GEO database

Comparison and overlap Analysis of multiple peak Files

First of all, we need to input the peak file, which supports two formats. The first is the BED format, which requires at least three columns of content to record the chromosome location of peak, as shown below.

Of course, there can also be extra columns, as long as they conform to the standard of BED format; the other is similar to the peak calling output of MACS, with the first behavior header, as shown below

Read the peak file through the function readPeaks, the usage is as follows

Peak