BAFfromGenotypes {GWASTools} | R Documentation |
This function calculates the B allele frequency and the log R ratio values for samples by either plate or by study.
BAFfromGenotypes(intenData, genoData, filename, file.type = c("gds", "ncdf"), min.n.genotypes = 2, call.method = c("by.plate", "by.study"), plate.name = "plate", block.size = 5000, precision="single", compress="LZMA_RA:1M", verbose = TRUE)
intenData |
|
genoData |
|
filename |
The name of the genotype GDS or netCDF file to create |
file.type |
The type of file to create ("gds" or "ncdf") |
min.n.genotypes |
The minimum number of samples for each genotype at any SNP in order to have non-missing B allele freqency and log R ratio. Setting this parameter to 2 or a similar value is recommended. |
call.method |
If call.method is 'by.plate', the B allele frequency and log R ratio are calculated for samples delineated by plates. This is the default method. If call.method is 'by.study', the calculation uses all samples at once. If a study does not have plate specifications, 'by.study' is the call.method that must be used. |
plate.name |
Character string specifying the name of the plate variable in intenData or genoData. By default, the plate.name is simply 'plate' but oftentimes there are variations, such as 'plateID' or 'plate.num'. |
block.size |
An integer specifying the number of SNPs to be loaded at one time. The recommended value is around 1000, but should vary depending on computing power. |
precision |
A character value indicating whether floating point numbers should be stored as "double" or "single" precision. |
compress |
The compression level for variables in a GDS file (see
|
verbose |
Logical value specifying whether to show progress information. |
Because this function can take a considerable amount of time and space, sufficient attention should be given to the value used for block.size
.
Caitlin McHugh
Peiffer D.A., Le J.M., Steemers F.J., Chang W., Jenniges T., and et al. High-resolution genomic profiling of chromosomal aberrations using infinium whole-genome genotyping. Genome Research, 16:1136-1148, 2006.
IntensityData
, GenotypeData
,
chromIntensityPlot
, BAFfromClusterMeans
## Not run: # create IntensityData and GenotypeData objects from netCDF library(GWASdata) data(affySnpADF) data(affyScanADF) nsamp <- nrow(affyScanADF) xyfile <- system.file("extdata", "affy_qxy.nc", package="GWASdata") xyNC <- NcdfIntensityReader(xyfile) xyData <- IntensityData(xyNC, snpAnnot=affySnpADF, scanAnnot=affyScanADF) genofile <- system.file("extdata", "affy_geno.nc", package="GWASdata") genoNC <- NcdfGenotypeReader(genofile) genoData <- GenotypeData(genoNC, snpAnnot=affySnpADF, scanAnnot=affyScanADF) # calculate BAF and LRR blfile <- tempfile() BAFfromGenotypes(xyData, genoData, blfile, file.type="ncdf", min.n.genotypes=2, call.method="by.plate", plate.name="plate") blNC <- NcdfIntensityReader(blfile) baf <- getBAlleleFreq(blNC) lrr <- getLogRRatio(blNC) close(xyData) close(genoData) close(blNC) file.remove(blfile) ## End(Not run)