methRatio: convert ampliconView objects to a table of methylation ratio

In BIMSBbioinfo/AmpliconBiSeq: analyzing amplicon bisulfite sequencing data

Description

convert ampliconView objects to a table of methylation ratio

Usage

methRatio(x,per.region=FALSE,asGRanges=TRUE,dup.resolve=TRUE,simple.tags=TRUE,coverage.th=0)

Arguments

x	an AmpliconViews object
per.region	logical, if FALSE base-pair methylation ratio (def:FALSE)
asGRanges	logical, if TRUE object returned is a GRanges object (def:TRUE)
dup.resolve	logical, if TRUE , and if per.region=FALSE, the duplicated CpGs will be resolved by taking the one with highest coverage. Since amplicon designs can overlap, there might be CpGs that are covered by different amplicon designs at the same time, this will result in duplicated CpGs in the resulting object. (def:TRUE)
simple.tags	logical. If TRUE, tags associated with amplicons will be output as a single column. If FALSE, a tag column will be output for each experiment.
coverage.th	default to 0. If this is set to a value larger than zero, the bases/regions that have have coverage below this value will have NA methylation and NA coverage.

Value

data frame or GRanges object with locations of CpGs and methylation ratio and coverage

Examples

# methRatio(a.list,per.region=FALSE,asGRanges=TRUE,dup.resolve=TRUE)

BIMSBbioinfo/AmpliconBiSeq documentation built on May 5, 2019, 10:25 a.m.