Good afternoon,
I am trying to analyse a set of CEL files from Affymetrix GenomeWideSNP 6.0
and get its LRR, FreqB and genotype (for all individuals and for all
chromosomes).
I have started with the vignettes "CRMA (v1): Total copy number analysis
using CRMA v1 (10K, 100K, 500K)" and "CRMA (v2): Estimation of total copy
numbers using the CRMA v2 method (10K-CytoScanHD)" since I am new in this
world of microarrays analysis.
But I didn't fine any way to retrieve the genotype I moved to "CRLMM
genotyping (100K and 500K)".
So, from both methods I can get the LRR and FreqB with extactCNT of with
extractTotalAndFraqB but only from the second one (CRLMM) I can use the
extractGenotypes (becouse the chiptype's crlmm model is required). On the
other hand when I try to create the crlmm model for GenomeWideSNP 6.0 the
following error succeed:
Exception: Cannot fit CRLMM model: Model fitting for this chip type is not
supported/implemented: GenomeWideSNP_6
at #02. CrlmmModel(ces, tags = "*,oligo")
- CrlmmModel() is in environment 'aroma.affymetrix'
at #01. process_dataset("GenomeWideSNP_6", "gal", verbose = TRUE)
- process_dataset() is in environment 'R_GlobalEnv'
Error: Cannot fit CRLMM model: Model fitting for this chip type is not
supported/implemented: GenomeWideSNP_6
So... Am I doing something wrong? If no, is there some way to get the full
set of data I need (sample's name, sample's position, chromosome, LRR,
FraqB and genotype) using a single method?
My full code-snippet:
library( 'aroma.affymetrix' )
write_table <- function( dataset, file_name ) {
[...]
}
process_dataset <- function( dataset_name chip_type ) {
cdf <- AffymetrixCdfFile$byChipType( chip_type );
csR <- AffymetrixCelSet$byName( dataset_name, cdf=cdf );
ces <- justSNPRMA( csR, normalizeToHapmap=TRUE, returnESet=FALSE );
crlmm <- CrlmmModel( ces, tags="*,oligo" );
units <- fit( crlmm, ram="oligo" );
callSet <- getCallSet( crlmm );
gi <- getGenomeInformation( cdf );
for( array in 1:length( csR ) ) {
ds <- NULL;
ce <- getFile( ces, array );
for( chr in chr_list ) {
chrunits <- getUnitsOnChromosome( gi, chromosome=chr );
chrnames <- getUnitNames( cdf, units=chrunits )
pos <- getPositions( gi, units=chrunits ); # / 1e6;
cf <- getFile( callSet, array );
calls <- extractGenotypes( cf, units=chrunits );
dta <- extractTotalAndFreqB( ce, units=chrunits );
theta <- dta[,"total"];
ceR <- getAverageFile( ces );
dataR <- extractTotalAndFreqB( ceR, units=chrunits );
thetaR <- dataR[,"total"];
l2r <- log2(theta/thetaR);
ds <- add_to_ds( chrnames, rep( chr, length( chrnames ) ),
pos, l2r, dta[,"FreqB"], calls );
}
colnames( ds ) <- c( "Name", "Chr", "Position", "Log.R.Ratio",
"B.Allele.Freq", "GType" );
write_table( ds, paste0( getName( ce ), ".txt" ) )
}
}
}
process_dataset( "GenomeWideSNP_6", "gal" )
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