parBE: Parallel Backward Elimination

In gada: Genome Alteration Detection Algorithm (GADA)

Description

This function performs backward elimination procedure after SBL segmentation for a collection of samples.

Usage

parBE(x, Samples, T, MinSegLen, verbose = TRUE, ...)

## S3 method for class 'summaryParGADA'
print(x, ...)
## S3 method for class 'parGADA'
labels(object, ...)
## S3 method for class 'summaryParGADA'
labels(object, ...)

Arguments

x	an object of class 'parGADA' obtained using 'setupParGADAIllumina' or 'setupParGADAaffy' functions
Samples	the samples to be analyzed
T	critical value of the backward elimination algorithm (see 'BackwardElimination' function)
MinSegLen	minimum number of probes each segment must contain (see 'BackwardElimination' function)
verbose	is information about each individual showed in the console? Default is TRUE
object	an object of class 'parGADA' or 'summaryParGADA'
...	other arguments passed through the function 'BackwardElimination'

Details

This function calls repeteadly to function 'BackwardElimination' after being used the function 'parSBL' 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

parSBL, 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.