get_peak_summit_seq: Get DNA sequence from peak summit region

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This function extract the DNA sequence around peak summit region from narrowPeak file

Usage

get_peak_summit_seq(
  file,
  peakFormat = "narrowPeak",
  sampleId = NULL,
  genome,
  length = 200,
  column_suffix = TRUE
)

Arguments

file	peak file generated by macs2
peakFormat	Peak file format. One of c("narrowPeak", "broadPeak", "bed") Default: narrowPeak
sampleId	sample ID
genome	BSgenome object
length	Length of the region. Default: 200
column_suffix	Whether to modify the column names to include sampleId. If TRUE, the new column names are of format: colName.sampleId

Value

A dataframe with three columns: name, summitRegion, summitSeq

Examples

summitSeq = get_peak_summit_seq("test.narropeak", "sampleId", BSgenome.Afumigatus.AspGD.Af293, 200)

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.