annotatePeaks

Runs DA pipeline and makes it ready for enrichment analyses

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data
analyses. This package combines different packages to have an ultimate package
for both data analyses and visualization of 'ATAC-seq' data. Methods are described in
'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.

Onur Karakaslar

cinaR

A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

Duygu Ucar

annotatePeaks function

<dl><dt>cp</dt>
<dd>bed formatted consensus peak matrix: CHR, START, STOP and raw peak counts (peaks by 3+samples)</dd>
<dt>reference.genome</dt>
<dd>genome of interested species. It should be 'hg38', 'hg19' or 'mm10'.</dd>
<dt>show.annotation.pie</dt>
<dd>shows the annotation pie chart produced with ChipSeeker</dd>
<dt>verbose</dt>
<dd>prints messages through running the pipeline</dd></dl>

Arguments

annotatePeaks — annotatePeaks

<dl>

<dt>cp</dt>
<dd>bed formatted consensus peak matrix: CHR, START, STOP and raw peak counts (peaks by 3+samples)</dd>


<dt>reference.genome</dt>
<dd>genome of interested species. It should be 'hg38', 'hg19' or 'mm10'.</dd>


<dt>show.annotation.pie</dt>
<dd>shows the annotation pie chart produced with ChipSeeker</dd>


<dt>verbose</dt>
<dd>prints messages through running the pipeline</dd>

</dl>

annotatePeaks: annotatePeaks

Description

Usage

Value

Arguments