downsample: Downsample analysis

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

Description

Downsample the CpG coverage matrix for saturation analysis

Usage

downsample(bs, dsRates = c(0.01, 0.02, 0.05, seq(0.1, 0.9, 0.1)),
  subSample = 1e+06, offset = 50000)

Arguments

bs	bsseq object
dsRates	downsampling rate. i.e. the probabaility of sampling a single CpG default is list of probabilities ranging from 0.01 to 1 0.01 0.02 0.05 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 For more continuous saturation curve dsRates can be changed to add more sampling rates
subSample	number of CpGs to subsample Default value is 1000000.
offset	how many CpGs to offset when subsampling Default value is set to be 50000, i.e. first 50000 CpGs will be ignored in subsampling.

Value

Data frame with the CpG coverage for each sample at each sampling rate

Examples

directory <- system.file("extdata/bismark_data", package='scmeth')
bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
scmeth::downsample(bs)

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