getReadMatrix: Extract methylation matrix from alignment file

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

Extract methylation matrix from alignment file

Description

Extract methylation matrix from alignment file

Usage

getReadMatrix(
  bamFile,
  genomeFile,
  bedFile,
  region,
  samtoolsPath = "",
  maxDepth = 10000
)

Arguments

bamFile	String with path to bam file with alignments of reads to genome
genomeFile	String with path to fasta file with genome sequence
bedFile	String with path to .bed file with locations of Cs to be evaluated
region	Genomic range of region for which to extract reads. It can also be a string denoting the region, e.g. "X:8069396-8069886"
samtoolsPath	Path to samtools executable (default="") if not in unix $PATH
maxDepth	Maximum number of reads to take for a given region (default=10,000)

Value

A matrix with reads as row names and C positions as column names. Every position in matrix has a value of 0 (non-converted C = methylated), 1 (converted C (T) = not methylated) or NA (undetermined)

jsemple19/methMatrix documentation built on Aug. 19, 2022, 3:57 p.m.