enrichPeakOverlap

queryPeak

target bed file(s) or folder that containing bed files or a list of GRanges objects

targetPeak

TxDb

pAdjustMethod

nShuffle

chainFile

pool

number of cores, see <a rd-options="parallel" href="/link/mclapply?package=ChIPseeker&version=1.8.6&to=parallel" data-mini-rdoc="parallel::mclapply">mclapply</a>

mc.cores

verbose


calculate overlap significant of ChIP experiments based on the genome coordinations


This package implements functions to retrieve the nearest genes
around the peak, annotate genomic region of the peak, statstical methods
for estimate the significance of overlap among ChIP peak data sets, and
incorporate GEO database for user to compare the own dataset with those
deposited in database. The comparison can be used to infer cooperative
regulation and thus can be used to generate hypotheses. Several
visualization functions are implemented to summarize the coverage of the
peak experiment, average profile and heatmap of peaks binding to TSS
regions, genomic annotation, distance to TSS, and overlap of peaks or
genes.

Guangchuang Yu

ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

enrichPeakOverlap function

number of cores, see <a rd-options='parallel' href='mclapply'>mclapply</a>

enrichPeakOverlap: enrichPeakOverlap

Description

Usage

Arguments

Value