BAFfromClusterMeans {GWASTools} | R Documentation |
This function calculates the B allele frequency and the log R ratio values from the mean R and theta values for each cluster.
BAFfromClusterMeans(intenData, filename, file.type = c("gds", "ncdf"), clusterMeanVars = c("tAA","tAB","tBB","rAA","rAB","rBB"), precision="single", compress="LZMA_RA:1M", verbose = TRUE)
intenData |
|
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
|
verbose |
Logical value specifying whether to show progress information. |
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.
Stephanie Gogarten, 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
, BAFfromClusterMeans
# 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)