interface_funcs: Functions/methods interfacing with other packages

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

Description

Provides the main functionality behing oligoMask. These functions/methods allow the user to apply variant masks to oligo classes such as GemeFeatureSet.

Usage

	## S4 method for signature 'GeneFeatureSet'
maskRMA(object, background=TRUE, normalize=TRUE, subset=NULL, target="core", mask.type=c("before.rma", "before.summary"), apply.mask=FALSE, mask.params=NULL)
	

Arguments

object	A valid object of class GeneFeatureSet (for now)
background	Logical-perform RMA background correction?
normalize	Logical-perform quantile normalization?
subset	To be implemented
target	Type of summarization to be performed (e.g. 'core' or 'probeset')
apply.mask	Boolean indicating whether the variant mask should be applied
mask.params	An object of class VariantMaskParams
mask.type	Either 'before.rma' or 'before.summary' where 'before.rma' carries out the masking before the RMA processing occurs while 'before.summary' performs masking after the background correction and normalization but before the summarization step via median polish.

Methods

maskRMA

signature(object = "GeneFeatureSet") Return a ExpressionSet object with the probes summarized at the level indicated by target using the RMA method. Probes determined to be unreliable are removed prior to the RMA calculations.

Author(s)

Daniel Bottomly

See Also

rma, GeneFeatureSet

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)
	
	masked.exprs <- maskRMA(SunGeneFS, apply.mask=TRUE, mask.params=var.mask.pars)

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