BAFfromClusterMeans {GWASTools} | R Documentation

## 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)

[Package GWASTools version 1.40.0 Index]