snpmap {SNPMaP}R Documentation

SNP Microarrays and Pooling

Description

Functions to process SNPMaP data from CEL files to Relative Allele Score summaries (rasS).

Usage

snpmap(cels = dir(pattern = ".[cC][eE][lL]$"), lowMemory = TRUE, set = 1,
        useMM = FALSE, normalize = FALSE, log.intensities = FALSE, ras.summary = qcMean,
        tempDir = ".", RUN = "cel2rasS", interactive=FALSE, ...)
msnpmap(cels = dir(pattern = ".[cC][eE][lL]$"), lowMemory = TRUE, set = 0,
        useMM = FALSE, normalize = FALSE, log.intensities = FALSE, ras.summary = qcMean,
        tempDir = ".", RUN = "cel2rasS", interactive=FALSE, ...)

Arguments

cels character; a vector of CEL files to use in the analysis
lowMemory logical; should the SNP data be stored on disk rather than in memory?
set numeric, a single number for snpmap or a vector for msnpmap; the probesets to include see SNPMaP.cdm-package. The special set=0 corresponds to all the sets on the array.
useMM logical; should mismatch probes be used in the analysis (if they are present on the array)?
normalize logical; should the probe intensities be quantile normalised across arrays?
log.intensities logical; use the natural log of the probe intensities?
ras.summary function to compute summary statistic for RAS scores on each chip. See SNPMaP-class.
tempDir character; writable directory to store the probe data if lowMemory=TRUE.
RUN character, name of a workflow function cel2*; see cel2ras().
interactive logical; should snpmap() prompt for CEL files (Windows only)?
... addtional arguments passed on to workflow function.

Details

snpmap() sets up the SNPMaP analysis and calls a workflow function to extract the data from the CEL files to 'raw' intensity data for all probes on the array (at any set), to a 'long' format matrix (one column per array), to a 'short' format matrix (one row per probeset), to 'ras' (a matrix of Relative Allele Scores, one per quartet, one row per probeset), or to 'rasS' (a matrix of RAS, one per probeset, one column per array). Specifying lowMemory=TRUE stores the data as a FileDoubleMatrix on disk rather than in memory.

Value

Object of class SNPMaP for snpmap(); list of SNPMaP objects for msnpmap().

Warning

snpmap() returns the SNPs from a single set on the array. For some arrays you will need to call snpmap() several times to access all the SNPs, or msnpmap(set=0).

See Also

SNPMaP-package.
SNPMaP.cdm-package.
SNPMaP-class for SNPMaP objects and methods.
cel2ras() for workflow functions.
disk2memory() to transfer SNPMaP objects between disk and memory.
cloneSNPMaP() to copy a SNPMaP object on disk.
writeSNPMaP() to write SNPMaP objects to text files.
norm(), the quantile normalization function.
logIntensities(), the function that logs the raw intensities.

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]