get_single_strand_matrix: Single Strand Metagene Matrix

In manschmi/RMetaTools: Tools For Metagene Analysis

Description

Creates metagene matrix for single bigwig file.

Usage

get_single_strand_matrix(bw, anno, upstream = 1000, downstream = 1000)

Arguments

bw	filename for bigwig file.
anno	GRanges object of regions to query.
upstream	bp upstream of anchor (default=1000)
downstream	bp downstream of anchor (default=1000)

Details

Loads the bed file, extracts the position of the anchor point and creates ranges from x bp upstream to x bp downstream. I upstream and downstream are both NULL, collects signal within region specified in anno.

Value

matrix with columns from most upstream to most downstream and rows are the individual regions from specified strand. rownames are set as name column from anno. colnames are set to relative position of each nt

Examples

bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
regions <- meta_regions(bedfile, 'TSS', 1000, 5000)
bw <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw", package = "RMetaTools")
mat <- get_single_strand_matrix(bw=bw, anno=regions, upstream=1000, downstream=5000)

manschmi/RMetaTools documentation built on Dec. 14, 2021, 4:33 a.m.