cpgDensity: Provides Coverage by the CpG density. CpG Density is defined...

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

Description

Provides Coverage by the CpG density. CpG Density is defined as the number of CpGs observed in certain base pair long region.

Usage

cpgDensity(bs, organism, windowLength = 1000, small = FALSE)

Arguments

bs	bsseq object
organism	scientific name of the organism of interest, e.g. Mmusculus or Hsapiens
windowLength	Length of the window to calculate the density
small	Indicator for a small dataset, cpg density is calculated more memory efficiently for large dataset but for small dataset a different quicker method is used Default value for window length is 1000 basepairs.

Value

Data frame with sample name and coverage in repeat masker regions

Examples

library(BSgenome.Hsapiens.NCBI.GRCh38)
directory <- system.file("extdata/bismark_data", package='scmeth')
bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
cpgDensity(bs, Hsapiens, 1000, small=TRUE)

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