readCdfUnitsWriteMap {affxparser} | R Documentation |
Generates an Affymetrix cell-index write map from a CDF file.
The purpose of this method is to provide a re-ordering of cell elements such that cells in units (probesets) can be stored in contigous blocks. When reading cell elements unit by unit, minimal file re-position is required resulting in a faster reading.
Note: At the moment does this package not provide methods to
write/reorder CEL files. In the meanwhile, you have to write
and re-read using your own file format. That's not too hard using
writeBin()
and readBin
().
readCdfUnitsWriteMap(filename, units=NULL, ..., verbose=FALSE)
filename |
The pathname of the CDF file. |
units |
An integer vector of unit indices specifying which units
to listed first. All other units are added in order at the end.
If NULL , units are in order. |
... |
Additional arguments passed to readCdfUnits (). |
verbose |
Either a logical , a numeric , or a Verbose
object specifying how much verbose/debug information is written to
standard output. If a Verbose object, how detailed the information is
is specified by the threshold level of the object. If a numeric, the
value is used to set the threshold of a new Verbose object. If TRUE ,
the threshold is set to -1 (minimal). If FALSE , no output is written
(and neither is the R.utils package required). |
A integer
vector
which is a write map.
Henrik Bengtsson (http://www.braju.com/R/)
To invert maps, see invertMap
().
readCel
() and readCelUnits
().
############################################################## if (require("AffymetrixDataTestFiles")) { # START # ############################################################## # Find any CDF file cdfFile <- findCdf() # Create a cell-index map (for writing) writeMap <- readCdfUnitsWriteMap(cdfFile) # Inverse map to be used to read cell elements such that, when read # read unit by unit, they are read much faster. readMap <- invertMap(writeMap) # Validate the two maps stopifnot(identical(readMap[writeMap], 1:length(readMap))) cat("Summary of the \"randomness\" of the cell indices:\n") moves <- diff(readMap) - 1 cat(sprintf("Number of unnecessary file re-positioning: %d (%.1f%%)\n", sum(moves != 0), 100*sum(moves != 0)/length(moves))) cat(sprintf("Extra positioning: %.1fGb\n", sum(abs(moves))/1024^3)) smallMoves <- moves[abs(moves) <= 25]; largeMoves <- moves[abs(moves) > 25]; layout(matrix(1:2)) main <- "Non-signed file moves required in unorded file" hist(smallMoves, nclass=51, main=main, xlab="moves <=25 bytes") hist(largeMoves, nclass=101, main="", xlab="moves >25 bytes") # Clean up layout(1) rm(cdfFile, readMap, writeMap, moves, smallMoves, largeMoves, main) ############################################################## } # STOP # ############################################################## ############################################################## if (require("AffymetrixTestDataFiles")) { # START # ############################################################## # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Function to read Affymetrix probeset annotations # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - readAffymetrixProbesetAnnotation <- function(pathname, ...) { # Get headers header <- scan(pathname, what="character", sep=",", quote="\"", quiet=TRUE, nlines=1); # Read only a subset of columns (unique to this example) cols <- c("Probe Set ID"="probeSet", "Chromosome"="chromosome", "Physical Position"="physicalPosition", "dbSNP RS ID"="dbSnpId"); colClasses <- rep("NULL", length(header)); colClasses[header %in% names(cols)] <- "character"; # Read the data (this is what takes time) df <- read.table(pathname, colClasses=colClasses, header=TRUE, sep=",", quote="\"", na.strings="---", strip.white=TRUE, check.names=FALSE, blank.lines.skip=FALSE, fill=FALSE, comment.char="", ...); # Re-order columns df <- df[,match(names(cols),colnames(df))]; colnames(df) <- cols; # Use "Probe Set ID" as rownames. Note that if we use 'row.names=1' # or similar something goes wrong. /HB 2006-03-06 rownames(df) <- df[[1]]; df <- df[,-1]; # Change types of columns df[[1]] <- factor(df[[1]], levels=c(1:22,"X","Y",NA), ordered=TRUE); df[[2]] <- as.integer(df[[2]]); df; } # readAffymetrixProbesetAnnotation() # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Main # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - for (zz in 1) { # Chip to be remapped chipType <- "Mapping50K_Xba240" annoFile <- paste(chipType, "_annot.csv", sep="") cdfFile <- findCdf(chipType) if (is.null(cdfFile) || !file.exists(annoFile)) break; # Read SNP location details snpInfo <- readAffymetrixProbesetAnnotation(annoFile) # Order by chromsome and then physical position o <- order(snpInfo[[1]], snpInfo[[2]]) snpInfo <- snpInfo[o,] rm(o) # Read unit names in CDF file unitNames <- readCdfUnitNames(cdfFile) # The CDF unit indices sorted by chromsomal position units <- match(rownames(snpInfo), unitNames) # ...and cell indices in the same order writeMap <- readCdfUnitsWriteMap(cdfFile, units=units) # Inverse map to be used to write cell elements such that, if they # later are read unit by unit, they are read in contiguous blocks. readMap <- invertMap(writeMap) # Clean up rm(chipType, annoFile, cdfFile, snpInfo, unitNames, units, readMap, writeMap) } # for (zz in 1) ############################################################## } # STOP # ##############################################################