setupParGADA: Parallel version of setupGADA

In isglobal-brge/R-GADA: Genome Alteration Detection Algorithm (GADA)

Description

This functions calls repeteadly to setupGADA to import raw data (pennCNV format) for several samples to R-GADA

Usage

setupParGADA(folder, files, MarkerIdCol=1,
             ChrNameCol=2, ChrPosCol=3,
             chrs=c(1:22, "X", "Y"),
             XY=TRUE, verbose=TRUE, 
             mc.cores=1, ...)

Arguments

folder	The folder where data is stored. Not required
files	The names of the files with Illumina data. Not required
MarkerIdCol	The column having marker ids in the pennCNV files. The defaul is 1
ChrNameCol	The column having chromosome names in the pennCNV files. The defaul is 2
ChrPosCol	The column having genomic position in the pennCNV files. The defaul is 3
chrs	A vector containg the available chromosomes. The default is c(1:22, "X", "Y")
XY	Do data have X and Y labels in annotation (instead of 23 and 24)? The default is TRUE
verbose	Should information about process be printed in the console? The default is TRUE
mc.cores	number of cores to be used when using multiple cores (see argument 'mc.cores' from 'mclapply' function of 'parallel' library)
...	Other arguments passed through 'setupGADA'

Details

See setupGADA

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, 2010;11:380.

See Also

setupParGADA, parSBL, parBE

Examples

 ## Not run: 
  See the vignette
 
## End(Not run) 

isglobal-brge/R-GADA documentation built on May 24, 2019, 5:03 a.m.