cel2ras {SNPMaP}R Documentation

SNPMaP workflows

Description

Workflow functions to process SNPMaP objects. Called by snpmap().

Usage

cel2raw(x, cels = x@chps, lowMemory = x@lowMemory, ...)
cel2long(x, cels = x@chps, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, ...)
cel2short(x, cels = x@chps, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, ...)
cel2ras(x, cels = x@chps, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, subtractMismatch = x@useMM, ...)
cel2rasS(x, cels = x@chps, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, subtractMismatch = x@useMM, FUN = x@summary, ...)
raw2long(x, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, tidy = FALSE, ...)
raw2short(x, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, tidy = FALSE, ...)
raw2ras(x, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, subtractMismatch = x@useMM, tidy = FALSE, ...)
raw2rasS(x, lowMemory = x@lowMemory, set = x@set, normalize = x@normalize,
        log.intensities = x@logInt, subtractMismatch = x@useMM, FUN = x@summary,
        tidy = FALSE, ...)
long2short(x, lowMemory = x@lowMemory, tidy = FALSE, ...)
long2ras(x, lowMemory = x@lowMemory, subtractMismatch = x@useMM, tidy = FALSE, ...)
long2rasS(x, lowMemory = x@lowMemory, subtractMismatch = x@useMM, FUN = x@summary,
                tidy = FALSE, ...)
short2ras(x, lowMemory = x@lowMemory, subtractMismatch = x@useMM, tidy = FALSE, ...)
short2rasS(x, lowMemory = x@lowMemory, subtractMismatch = x@useMM, FUN = x@summary,
                tidy = FALSE, ...)
ras2rasS(x, lowMemory = x@lowMemory, FUN = x@summary, tidy = FALSE, ...)

Arguments

x An object of class SNPMaP.
cels character; a vector of the CEL files to be included.
lowMemory logical; should the SNP data be stored on disk rather than in memory?
tidy logical; if the data is stored on disk, should the old FileDoubleMatrix be unlinked?
set numeric; the set of probesets to include. See SNPMaP.cdm-package.
normalize logical; quantile normalize probe intensities across arrays.
log.intensities logical; take natural log of probe intensities.
subtractMismatch logical; subtract mismatch probe intensities if available from perfect match intensities.
FUN function; function to compute summary statistic for RAS on each chip. See SNPMaP-class.
... additional arguments passed to other workflow and internal functions.

Details

The workflow functions work by calling cel2raw(), raw2long(), long2short(), short2ras(), ras2rasS().

Value

Object of class SNPMaP.

See Also

SNPMaP-package, SNPMaP.cdm-package, SNPMaP-class, snpmap(), norm(), logIntensities()

Examples

## Not run: 
 ## Getting started
 ## Creates the 'raw' SNPMaP object x on disk with mismatch probes included
 x<-snpmap(useMM=TRUE, RUN='cel2raw', lowMemory=TRUE)
 ## Print a summary of the SNPMaP object
 summary(x)
 ## Add a comment (prints in the summary)
 comment(x)<-'High and low extreme pools from January'
 ## View pseudo image to screen for artefacts
 image(x)
 ## Plot probe intensities
 plot(x, FUN=log)
 boxplot(x, FUN=log)
 ## tidy=TRUE removes the FileDoubleMatrix from the old x to keep the disk tidy
 x<-raw2ras(x, tidy=TRUE)
 ## Plot Relative Allele Scores
 plot(x)
 ## Default tidy=FALSE does not remove the original FileDoubleMatrix from disk
 ## Useful if you want to keep x (no side effects)
 y<-ras2rasS(x)
 ## View the first ten rows
 as.matrix(y[1:10,])
 ## View a set of SNPs
 as.matrix(y[c("SNP_A-4192909", "SNP_A-4192918"),])
 ## Transfer the SNPMaP object from disk to memory
 y<-disk2memory(y, tidy=TRUE)
 ## Run the analysis again from CEL files to RAS summaries without viewing intermediate stages
 ## This time in memory (may require a lot of RAM)
 z<-snpmap(useMM=TRUE, RUN='cel2rasS', lowMemory=FALSE)
 plot(z)
 ## Get the RAS summary scores as a standard matrix
 rasSummaries<-as.matrix(z)
 ## Read all the sets into a list
 allSets<-msnpmap(set=0)
## End(Not run)

[Package SNPMaP version 1.0.2 Index]