deq: DEQ

In al-mcintyre/DEQ: A package to conveniently run DESeq2, edgeR, and QNB for the detection of differential methylation in MeRIP/m6A-seq data.

Description

A package to conveniently run DESeq2, edgeR, and QNB for the detection of differential methylation in MeRIP/m6A-seq data.

Usage

deq(input.bams, ip.bams, treated.input.bams, treated.ip.bams, peak.files,
  gtf, paired.end = FALSE, outfi = "deq_results.txt", tool = "deq",
  compare.gene = TRUE, readlen = 100, fraglen = 100, nthreads = 1)

Arguments

input.bams	vector of control input bam files
ip.bams	vector of control IP bam files
peak.files	vector of peak file names
gtf	location of a gtf file for annotations
paired.end	boolean indicating whether reads were paired end (defaults to FALSE)
outfi	output file name (defaults to deq.results.txt)
tool	which tools to run (options: any combination of d, e, and q; defaults to all: 'deq')
compare.gene	whether to calculate changes in gene expression for comparison (highly recommended, defaults to TRUE)
readlen	average read length for the data (defaults to 100)
fraglen	average fragment length for the data (defaults to 100) – (fraglen-readlen) is used to calculate the extension of reads for counting
nthreads	number of threads to run on (defaults to 1)
input.bams	vector of treatment input bam files
ip.bams	vector of treatment IP bam files

Value

GRanges object with peaks and estimated changes

al-mcintyre/DEQ documentation built on Jan. 21, 2020, 5:38 a.m.