runSingleNewSample: Run a single new sample after modeling complete

In GarrettJenkinson/borealis: Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Run a single new sample after modeling complete

Description

Run a single new sample after modeling using runBorealis has already been completed in a cohort of samples. It will not rebuild the models and only predict using previously estimated model specified by modelFile.

Usage

runSingleNewSample(inFile, outFile, minObsDepth=10, modelFile="CpG_model.csv")

Arguments

inFile	character(1) File name (including full path if not current working directory) to the bismark coverage file.
outFile	character(1) File name (including full path if not current working directory) for the sample's modeling outputs. If NULL is provided, no outputs will be written to disk.
minObsDepth	(optional) numeric(1) Minimum depth of coverage in this sample for a modeling output/p-value to be produced at a given CpG.
modelFile	(optional) character(1) File name (including full path if not current working directory) for the model files (built by running runBorealis function).

Value

Returns a GRanges object with modeling results.

Examples

extdata <- system.file("extdata", package="borealis")
outdir <- tempdir()
gr <- runSingleNewSample(file.path(extdata,'bismark','patient_72',
                            'patient_72.gz'),file.path(outdir,'output.txt'),
                            modelFile=file.path(extdata,'CpG_model_chr14.csv'))

GarrettJenkinson/borealis documentation built on Jan. 1, 2023, 6:16 a.m.