summarizeBsSeqOver {biscuiteer} | R Documentation

## 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)

[Package biscuiteer version 1.4.0 Index]