featureCoverage: Coverage based on the genomic feature

Description Usage Arguments Value Examples

View source: R/featureCoverage.R

Description

Provides Coverage metrics for the sample by each genomic features provided by the user

Usage

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featureCoverage(bs, features, genomebuild)

Arguments

bs

bsseq object

features

list of genomic features, e.g. genes_exons, genes_introns, cpg_islands, cpg_shelves Names are based on the annotatr packages, so all the features provided by the annotatr package will be supported in this function

genomebuild

reference alignment, i.e. mm10 or hg38

Value

a data frame with genomic feature names and the number of CpG covered in each feature

Examples

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directory <- system.file("extdata/bismark_data", package='scmeth')
bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
featureCoverage(bs, c('cpg_islands', 'cpg_shores'), 'hg38')

scmeth documentation built on Nov. 8, 2020, 6:21 p.m.