BAFfromGenotypes: B Allele Frequency & Log R Ratio Calculation

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

B Allele Frequency & Log R Ratio Calculation

Description

This function calculates the B allele frequency and the log R ratio values for samples by either plate or by study.

Usage

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)

Arguments

intenData	IntensityData object holding the X and Y intensity data from which the B allele frequency and log R ratio are calculated.
genoData	GenotypeData object.
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 add.gdsn for options.
verbose	Logical value specifying whether to show progress information.

Details

Because this function can take a considerable amount of time and space, sufficient attention should be given to the value used for block.size.

Author(s)

Caitlin McHugh

References

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.

See Also

IntensityData, GenotypeData, chromIntensityPlot, BAFfromClusterMeans

Examples

## 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)

smgogarten/GWASTools documentation built on May 18, 2024, 1:19 a.m.