BAFfromClusterMeans: 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 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="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.
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.

Author(s)

Stephanie Gogarten, 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, BAFfromClusterMeans

Examples

# 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)

smgogarten/GWASTools documentation built on Nov. 10, 2024, 9:54 p.m.