interface_funcs: Functions/methods interfacing with other packages

Description Usage Arguments Methods Author(s) See Also Examples

Description

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

Usage

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	## 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

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	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 12, 2017, 9:05 p.m.