poorBisulfiteConversion: Find bisulfite conversion rate of Cs in non-methylated...

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

Find bisulfite conversion rate of Cs in non-methylated context

Description

Use bedfile with positons of Cs that are in non-methylated context to obtain stats about the number of informative Cs and conversion status of Cs per read

Usage

poorBisulfiteConversion(
  bamFile,
  genomeFile,
  bedFileC,
  bedFileG,
  regionGR,
  samtoolsPath = ""
)

Arguments

bamFile	String with path to bam file with alignments of reads to genome
genomeFile	String with path to fasta file with genome sequence
bedFileC	String with path to .bed file with locations of Cs to be evaluated (for forward strand calls)
bedFileG	String with path to .bed file with locations of Gs to be evaluated (for reverse strand calls)
regionGR	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

Value

A data frame with the names of the reads, the count of the number of informative Cs per region (not NAs), the maximum number of possible Cs in the regon, and the fraction of the informative Cs which have been bisulfite converted

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