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Last data update: 2014.03.03

R: B Allele Frequency & Log R Ratio Calculation

BAFfromClusterMeans

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="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.

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.

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)

Results


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> library(GWASTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/BAFfromClusterMeans.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BAFfromClusterMeans
> ### Title: B Allele Frequency & Log R Ratio Calculation
> ### Aliases: BAFfromClusterMeans
> ### Keywords: datagen manip
> 
> ### ** 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)
[1] TRUE
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>