featureCoverage: Coverage based on the genomic feature

In aryeelab/scmeth: Functions to conduct quality control analysis in methylation data

Description

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

Usage

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

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

aryeelab/scmeth documentation built on June 15, 2019, 8:02 p.m.