summarizeBsSeqOver: Summarize methylation over provided regions

In trichelab/biscuiteer: Convenience Functions for Biscuit

Summarize methylation over provided regions

Description

Used for bsseq objects. Mostly a local wrapp for getMeth.

Usage

summarizeBsSeqOver(bsseq, segs, dropNA = FALSE, impute = FALSE)

Arguments

bsseq	The bsseq object to summarize
segs	Regions to summarize over (GRanges object, no GRangesList yet)
dropNA	Whether to drop rows if more than half of samples are NA (DEFAULT: FALSE)
impute	Whether to impute NAs/NaNs (DEFAULT: FALSE)

Value

   A matrix of regional methylation fractions

Examples

  orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz",
                          package="biscuiteer")
  orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz",
                          package="biscuiteer")
  bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf,
                      merged = FALSE)

  reg <- GRanges(seqnames = rep("chr11",5),
                 strand = rep("*",5),
                 ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7),
                                  end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7))
                )
  summary <- summarizeBsSeqOver(bsseq = bisc, segs = reg, dropNA = TRUE)

trichelab/biscuiteer documentation built on March 4, 2024, 12:22 a.m.