tssMap: tssMap

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

Description

Calculate chip seq matrix around given tss. Flip starnd if strand is "-".

Usage

tssMap(query, anndf, left = -5000, right = 5000, bin_width = 25)

Arguments

query	A coverage RLEList. 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 import Bed file of peak into GRanges object. 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', 'start', 'end', 'strand'. The function will find TSS based on the strand information.
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.

Value

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

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