fiberseqBedToBigwig: Convert fiberseq bed file to bigwig

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

Convert fiberseq bed file to bigwig

Description

Processes data from bed file that is the output of Andrew Stergachis fiberseq scripts where each row is a fiber and the final columns indicate methylated positions in that fiber. Output is: 1) the original GRanges with all invalide fibers removed and with additional column denoting fraction methylation, 2) A new GRanges with all valid A/T postions and their fraction methylation.

Usage

fiberseqBedToBigwig(
  bedGR,
  genome = BSgenome.Celegans.UCSC.ce11::Celegans,
  ATpositionGR = NULL,
  minSubreadCov = 10,
  minReadCov = 5
)

Arguments

bedGR	GRanges object of fiberseq output (bed) imported into R
genome	BSgenome object for your organism with UCSC style seqinfo (Default is C. elegans ce11)
ATpositionGR	GRanges object with position of all As and Ts in genome
minSubreadCov	Minimum coverage of the read with subreads (default=10)
minReadCov	Minimum read coverage per genomic position (default=5)

Value

List of two GRanges: The first is the original bedGR but with additonal metadata columns for fraction methylation per fiber. The second contains all the A/T sites along the genome for which a valid fraction methylation could be calculated.

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