Description Usage Arguments Value Examples
Downsample the CpG coverage matrix for saturation analysis
1 2 | downsample(bs, dsRates = c(0.01, 0.02, 0.05, seq(0.1, 0.9, 0.1)),
subSample = 1e+06, offset = 50000)
|
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. |
Data frame with the CpG coverage for each sample at each sampling rate
1 2 3 | directory <- system.file("extdata/bismark_data", package='scmeth')
bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
scmeth::downsample(bs)
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