txt2GR: Function to filter a ChIP-Seq input.

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

Function to filter a ChIP-Seq output (in .narrowpeak or MACS's peaks.bed formats) and then store the peak coordinates in a GenomicRanges object, associated to its metadata.

Usage

txt2GR(fileTable, format, fileMetaData, alpha = NULL)

Arguments

fileTable	data frame from a txt/tsv/bed file
format	'narrowpeak', 'macs1.4' or 'macs2'. narrowPeak fields: 'chrom','chromStart','chromEnd','name','score','strand','signalValue', 'pValue','qValue','peak' macs1.4 fields: 'chrom','chromStart','chromEnd','name','-10*log10(p-value)' macs2 fields: 'chrom','chromStart','chromEnd','name','-log10(p-value)'
fileMetaData	Data frame/matrix/array contaning the following fields: 'Name','Accession','Cell','Cell Type','Treatment','Antibody', 'TF'.
alpha	max p-value to consider ChIPseq peaks as significant and include them in the database. By default alpha is 0.05 for narrow peak files and 1e-05 for MACS files

Value

The function returns a GR object generated from the ChIP-Seq dataset input.

Examples

data('ARNT.peaks.bed','ARNT.metadata',package = 'TFEA.ChIP')
ARNT.gr<-txt2GR(ARNT.peaks.bed,'macs1.4',ARNT.metadata)

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.