getNearestFeatureIndicesAndDistances

peaks

features

logical, whether find nearest gene in the same strand

sameStrand

logical, whether ignore overlap of TSS with peak

ignoreOverlap

logical, if True only annotate gene at the 3' of the peak.

ignoreUpstream

logical, if True only annotate gene at the 5' of the peak.

ignoreDownstream

overlap


get index of features that closest to peak and calculate distance


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.

getNearestFeatureIndicesAndDistances: getNearestFeatureIndicesAndDistances

Description

Usage

Arguments

Value