Dear all,
I'm processing a set of ~200 SNP6 .cel files and then performing
segmentation with CBS. But I would like to know how to extract the data
points data-frame that is used as input to DNAcopy CBS.
The code is as below:
# install.packages('aroma.affymetrix', repos='http://cran.us.r-project.org')
library("aroma.affymetrix")
# Logs
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
# Reduce decimal places to minimize space
options(digits=4)
print('Options configured')
# -- SNP6 cancer cell lines preprocessing with CRMA (v2)
gsT <- doCRMAv2("cancer_lines", chipType="GenomeWideSNP_6,Full",
verbose=verbose)
print('cancer_lines CRMAv2 done.')
# -- Segmentation (CBS)
sm <- CbsModel(gsT)
fit(sm, verbose=verbose)
print('CbsModel done.')
# -- Export segmentation
pathname <- writeRegions(sm, verbose=verbose)
print('Exported done.')
I would like to extract the gsT as a data.frame in the format that is used
in DNAcopy:
> library(DNAcopy)
> data(coriell)
> head(coriell)
Clone Chromosome Position Coriell.05296 Coriell.13330
1 GS1-232B23 1 0 NA 0.207470
2 RP11-82d16 1 468 0.008824 0.063076
3 RP11-62m23 1 2241 -0.000890 0.123881
4 RP11-60j11 1 4504 0.075875 0.154343
5 RP11-111O05 1 5440 0.017303 -0.043890
6 RP11-51b04 1 7000 -0.006770 0.094144
Thank you in advance,
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