exportToBED: Export segments to BED format

In gada: Genome Alteration Detection Algorithm (GADA)

Description

Export information about altered segments to BED format

Usage

exportToBED(x, num=300, strand="+", col.gain="0,255,255", col.loss="255,0,0", file="BED.txt")

Arguments

x	An object of class 'summaryparGADA'
num	Number that goes to the score number
strand	What to put on the strand field (default "+")
col.gain	Color of the bed element for copy number gain (default "0,255,255")
col.loss	Color of the bed element for copy number loss (default "255,0,0")
file	The name of the file to be saved. The default is 'BED.txt'

Value

No return value, just a file is produced

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, parSBL

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)

###
### Third step
### 

# summaryze all samples
allSamples<-summary(myExample)

# export to BED
exportToBED(allSamples)


## End(Not run)

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