peakMap: peakMap

In xons/chipMap: Make heatmap of High throughput sequencing data

Description

Calculate chip seq matrix around the centre of given peaks.

Usage

peakMap(query, anndf, left = -5000, right = 5000, bin_width = 25,
  sortByWidth = FALSE)

Arguments

query	A coverage RLE. This can be get from a bigWig file using bw2coverage function in this package. BigWig file can be generated from Bam file using bamtools and bedtools. Or a peak GRanges. This can be get from Bed file of peak using bed2gr function in this package. If the query is a peak GRanges, the output will be a enrichment profile instead of a coverage heatmap.
anndf	A data frame contains columns 'seqnames', 'peak_start', 'peak_end', 'strand'. The function will find peak center. 'strand' can be '*'. Flip strand if strand is "-".
left	Specify the window around TSS to be calculate. Default is -5 kb to 5 kb.
right	Specify the window around TSS to be calculate. Default is -5 kb to 5 kb.
bin_width	Specify the bin size to smooth and compress the window. Default is 25.
sortByWidth	If sort by the peak width or not. Default if FALSE.

Value

A matrix with each line as a region around each peak centre and each column is a bin.

xons/chipMap documentation built on May 4, 2019, 1:25 p.m.