make_coverage_matrix: make_coverage_matrix

In skummerf/GenomicWidgets: interactive visualization of genomics data

Description

Makes coverage matrix based on bam or bigwig inputs

Usage

make_coverage_matrix(inputs, ranges, input_names = names(inputs),
  binsize = 1, format = c("auto", "bigwig", "bam"), up = 0, down = 0)

Arguments

inputs	filenames of bigwig or bam
ranges	ranges for which to compute coverage within
input_names	names to associate with input bigwig or bam files, used for naming assays in resulting SummarizedExperiment object
binsize	binsize to bin coverage
format	format of files, default is auto
up	basepairs upstream of center to use
down	basepairs downstream of center to use

Details

up and down are 0 by default – if not specified, actual range is used. All ranges must be of equal width. If up and/or down are provided, then the center of the range and up basepairs upstream and down basepairs downstream are used.

Value

RangedSummarizedExperiment

Author(s)

Alicia Schep

Examples

library(GenomicRanges)
# First read in some sample data
genomation_dir <- system.file("extdata", package = "genomationData")

samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
samp.info <- read.table(samp.file, header=TRUE, sep='\t', 
                       stringsAsFactors = FALSE)
samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)

ctcf.peaks = genomation::readBroadPeak(system.file("extdata",
               "wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz",
               package = "genomationData"))
ctcf.peaks = ctcf.peaks[seqnames(ctcf.peaks) == "chr21"]
ctcf.peaks = ctcf.peaks[order(-ctcf.peaks$signalValue)]
ctcf.peaks = resize(ctcf.peaks, width = 1000, fix = "center")

# Make the coverage matrices
mats <- make_coverage_matrix(samp.info$fileName[1:3], ctcf.peaks, 
                     up = 500, down = 500, binsize = 25)

# Benchmarking speed of make_coverage_matrix compared to ScoreMatrixList
# function from genomation
## Not run: 
bm <- microbenchmark::microbenchmark(ctcf_mats = 
                             make_coverage_matrix(samp.info$fileName[1:3], 
                                                    ctcf.peaks, 
                                                   up = 500, down = 500, 
                                                    binsize = 25), 
                             geno = ScoreMatrixList(samp.info$fileName[1:3], 
                                              ctcf.peaks, bin.num = 1000/25),
                             times = 5)

bm

plot(bm)
## End(Not run)

skummerf/GenomicWidgets documentation built on May 31, 2019, 6:16 p.m.