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

Description Usage Arguments Value Examples

View source: R/cpgDensity.R

Description

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

Usage

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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

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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.