filterOutVariants: Filter out variants from 'MethPat' object.

In PeteHaitch/MethylationTuples: Tools for analysing methylation patterns at genomic tuples

Description

Filter out variants from MethPat object.

Usage

filterOutVariants(methpat, vcfs, remove = FALSE,
  verbose = getOption("verbose"), bpparam = bpparam())

Arguments

methpat	A MethPat object.
vcfs	A named character vector with the paths of the VCFs containing the variant calls. Currently only VCFs created by Bis-SNP are supported and it is required that there is one VCF per sample and that the order of vcfs corresponds to the samples in methpat (i.e., identical(names(vcfs), colnames(methpat) is TRUE).
remove	A logical(0). If TRUE rows of the MethPat object where all samples have a variant are removed from the object entirely, otherwise these are retained, albeit with the assay counts set to NA.
verbose	A logical(1) indicating whether progress should be reported via calls to message.
bpparam	A bpparam object specifying the parallelisation strategy, if any. See below for a discussion of parallelisation options available with readMethtuple.

Value

An updated version of the MethPat object, where variants have had their corresponding assays counts set to NA. Tuples where all samples are NA are retained (unless remove is TRUE).

Parallelisation

Parallelisation of filterOutVariants is partially supported. VCFs are read-in and processed in parallel, where appropriate. Parallelisation uses the BiocParallel package. By default this uses a MulticoreParam() instance or the user's preferred back-end if they have used register. Please consult the BiocParallel documentation for details on registering a parallel backend and parallelisation support available on different operating systems.

Examples

## Not run: 
## TODO

## End(Not run)

PeteHaitch/MethylationTuples documentation built on May 8, 2019, 1:30 a.m.