getLRR: Obtain LRR from RGset

In sean-cho/Epicopy: Get CNV information from 450K array

Description

Returns a matrix containing the log R ratios (LRR) of samples to reference set. Input file has to be an RGset. Normals can be defined by the user (see details).

Usage

getLRR(rgSet, Normals = NULL, sampNames = NULL, QN = FALSE,
  Ref = "mode", mode.bw = 0.1, mode.method = "naive", normal.cnv = TRUE,
  mean.center = TRUE, filterProbes = FALSE, retainedProbes = NULL,
  keep_fnobj = FALSE, fn_output = NULL, ...)

Arguments

rgSet	RGChannelSet object containing samples of interest
Normals	Either (1) RGChannelSet of normals (reference set), (2) a logical or numeric vector denoting the normals in the input rgSet, (3) a character of 'thyroid', 'lung', 'breast', or 'all' denoting reference set included in Epicopy, or (4) defaults to NULL, which uses all normals in Epicopy.
sampNames	A character vector giving sample names. Defaults to NULL, which uses pData(rgSet)$Sample_Name.
QN	Logical. Perform probe type specific quantile normalization of reference set.
Ref	'mode' or 'median'. Method to calculate reference intensity. Defaults to mode using the modeest package.
mode.bw	If Ref = 'mode', uses this bw to estimate the mode. Defaults to 0.1.
mode.method	If Ref = 'mode', uses this method to estimate the mode. Defaults to 'naive'.
normal.cnv	Logical. Return LRR for reference set.
mean.center	Logical. Perform mean centering of final data.
filterProbes	Logical. Filter probe by TCGA defined 450K probes adjacent to a known SNP.
retainedProbes	Character. IF filterProbes is TRUE, denotes probes to keep. If NULL, uses probes retained by TCGA.
keep_fnobj	Logical. Save functional normalized object as rda.
fn_output	Directory for fnobject. Defaults to current directory.
...	Passes argument to preprocessFunnorm.

Details

getLRR Preprocess RGset and obtain LRR for samples against a reference set.

GetLRR takes RGset as an argument as an input.

Normals/Reference samples can be defined multiple ways. Defaults to NULL which uses all the normals incorporated by the Epicopy package (see next paragraph). Providing an RGset will BiocGenerics::combine(rgSet, Normals) to get a dataset. Providing a logical/numeric vector will subset the rgSet into query and reference, with TRUE/numbers representing reference samples. Users can also specify one of 'thyroid', 'breast', 'lung', or 'all' to use Epicopy normals.

Epicopy normals are compiled using solid normal tissue methylation microarrays from TCGA.

Value

Matrix containing LRR values.

See Also

preprocessFunnorm RGChannelSet-class

Examples

# Get LRR
data(data_vignette)
# Median is used for quick calculation
res_lrr <- getLRR(epi_rg, Normals = NA, Ref = 'median')

sean-cho/Epicopy documentation built on May 29, 2019, 4:24 p.m.