cel2ras {SNPMaP} | R Documentation |
Workflow functions to process SNPMaP
objects. Called by snpmap()
.
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, ...)
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. |
The workflow functions work by calling cel2raw()
, raw2long()
, long2short()
,
short2ras()
, ras2rasS()
.
Object of class SNPMaP
.
SNPMaP-package
,
SNPMaP.cdm-package
,
SNPMaP-class
,
snpmap()
,
norm()
,
logIntensities()
## 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)