snpmap {SNPMaP} | R Documentation |
Functions to process SNPMaP data from CEL files to Relative Allele Score summaries (rasS).
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, ...)
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. |
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.
Object of class SNPMaP
for snpmap()
; list of SNPMaP
objects for msnpmap()
.
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)
.
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.
## 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)