enrichAnnoOverlap

queryPeak

target bed file(s) or folder containing bed files

targetPeak

TxDb

pAdjustMethod

chainFile

restrict nearest gene annotation by distance cutoff

distanceToTSS_cutoff


calcuate overlap significant of ChIP experiments based on their nearest gene annotation


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.

enrichAnnoOverlap: enrichAnnoOverlap

Description

Usage

Arguments

Value