parSBL: Parallel SBL segmentation

In gada: Genome Alteration Detection Algorithm (GADA)

Description

This function perform SBL segmentation for a collection of samples.

Usage

parSBL(x, Samples, estim.sigma2, aAlpha, verbose = TRUE, ...)

Arguments

x	an object of class 'parGADA' obtained using 'setupParGADAIllumina' or 'setupParGADAaffy' functions
Samples	the samples to be analyzed
estim.sigma2	array noise level (see 'SBL' function)
aAlpha	sparseness hyperparameter (see 'SBL' function)
verbose	is information about each individual showed in the console? Default is TRUE
...	other arguments passed through the function 'SBL'

Details

This function calls repeteadly to function 'SBL' to obtain all segments for each sample. It can be parallelized when multiple processors are available. This has been implemented using 'snow' package: http://www.sfu.ca/sblay/R/snow.html. See vignettes for further details

Value

This function saves the segments for each sample in a directory called SBL

References

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

See Also

parBE, setupParGADAIllumina, setupParGADAaffy

Examples

## Not run: 
###
### First step (required)
### 

# Read data 
# a folder called rawData containing a file for each individual is required

# Illumina data
myExample<-setupParGADAIllumina(log2ratioCol=4, NumCols=5)

# Affymetrix data
myExample<-setupParGADAaffy(log2ratioCol=4, NumCols=5)

###
### Second step
### 

# segmentation for all samples
parSBL(myExample, estim.sigma2=TRUE, aAlpha=0.8)
parBE(myExample,T=8, MinSegLen=8)

## End(Not run)

gada documentation built on May 2, 2019, 6:10 p.m.