VariantMaskParams: Class '"VariantMaskParams"'

In dbottomly/oligoMask: Tools for masking out problematic Affymetrix probes using VCF files and the oligo package

Description

A class containing the parameter values used for the filtering procedure.

Objects from the Class

Objects can be created by calls of the form new("VariantMaskParams", ...) or more conveniently through the VariantMaskParams constructor function as VariantMaskParams(var.db, geno.filter=FALSE, rm.unmap=TRUE, rm.mult=TRUE, mask.type="static").

Slots

mask.type:

Object of class "character" Type of mask, currently only the 'static' mask is available

geno.filter:

Object of class "logical" indicating whether only the probes overlapping the high quality genotypes be used (default is FALSE)

rm.unmap:

Object of class "logical" indicating whether the probes that are unmapped should be removed as well (default is TRUE)

rm.mult:

Object of class "logical" indicating whether the probes that map to multiple locations should be removed as well (default is TRUE)

oligo.probe.id:

Object of class "character" indicating the database column that the oligo package uses to denote the probe ID

var.db:

Object of class "VcfDB" corresponding to the VCF database to be used for masking

Methods

getProbeDf

signature(object = "VariantMaskParams"), gene.fs, target, sortBy="fsetid": Retrieve a data.frame describing the probe-(meta)probeset relationships of the probes not masked out based off the database connection in gene.fs and the summary type specified in target currently either 'core' or 'probeset'.

maskDb

signature(obj = "VariantMaskParams"): Retrieve the filename of the variant database

validProbeQuery

signature(object = "VariantMaskParams"), target, should.add=TRUE: Returns an SQLite query to be used for selecting the probes to be masked out and excluded from the basic query performed by oligo.

Author(s)

Daniel Bottomly

See Also

create.sanger.mouse.vcf.db, VcfDB

Examples

data(SunGeneFS)
temp.vcf.db <- new("VcfDB", db.path=om.db.file(), tbsl=SangerTableSchemaList())
var.mask.pars <- new("VariantMaskParams", var.db=temp.vcf.db)

validProbeQuery(var.mask.pars, target="core")

probe.df <- getProbeDf(var.mask.pars, gene.fs=SunGeneFS, target="core")
head(probe.df)

maskDb(var.mask.pars)

dbottomly/oligoMask documentation built on May 15, 2019, 1:22 a.m.