BAFfromClusterMeans: B Allele Frequency & Log R Ratio Calculation

Description

This function calculates the B allele frequency and the log R ratio values from the mean R and theta values for each cluster.

Usage

BAFfromClusterMeans(intenData, filename, file.type = c("gds", "ncdf"), clusterMeanVars = c("tAA","tAB","tBB","rAA","rAB","rBB"),
	            precision="single", compress="ZIP_RA", 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.

filename

The name of the genotype GDS or netCDF file to create

file.type

The type of file to create ("gds" or "ncdf")

clusterMeanVars

Character vector indicating the names of the cluster mean columns in the SNP annotation of intenData. Must be in order (tAA,tAB,tBB,rAA,rAB,rBB).

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

This function calculates the B allele frequency and the log R ratio values from the mean R and theta values for each cluster and writes them to a GDS or NetCDF file.

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.

Examples

Run this code

# create IntensityData object from GDS
library(GWASdata)
xyfile <- system.file("extdata", "illumina_qxy.gds", package="GWASdata")
xy <- GdsIntensityReader(xyfile)
data(illuminaSnpADF)
xyData <- IntensityData(xy, snpAnnot=illuminaSnpADF)

# calculate BAF and LRR and store in GDS file
blfile <- tempfile()
BAFfromClusterMeans(xyData, blfile, file.type="gds", verbose=FALSE)

# read output
bl <- GdsIntensityReader(blfile)
baf <- getBAlleleFreq(bl)
lrr <- getLogRRatio(bl)

close(xy)
close(bl)
file.remove(blfile)