TilingCelFiles2Probesets {AffyTiling} | R Documentation |
TilingCelFiles2Probesets extracts intensity data from a group of CEL files and returns annotated intensities using information from a BPMAP file. Options can be set to limit the analysis to certain genomic features or regions of interest,thus requiring less memory and computing time.
Returns a matrix, where rows represent probe sets and columns represent the following: –Unique probeset ID ("chromosome-first probe START position-last probe END position") –Probe start position (in genomic coordinates) –Chromosome –Average normalized intensity for sample 1 –Average normalized intensity for sample 2 ... –Average normalized intensity for sample N
Note that unlike AnalyzeTilingCelFiles, this function reports only 1 average value for all probes in each interval.
TilingCelFiles2Probesets(CEL_filenames, BPMAP_filename, outfilename=NULL, iID=NULL, iCHR, iSTART, iEND, IgnoreBpmapCelPlatformMismatch=FALSE)
CEL_filenames |
A character vector of the path to all CEL file(s) in the analysis. |
BPMAP_filename |
The path to the BPMAP file which describes the arrays specified in the cel files. |
outfilename |
If specified, the function writes a tab-separated table of normalized intensities. |
iID |
Vector of IDs for each interval specified. If NULL (default) creates a unique ID for each interval of the form: "CHR-START-END". |
iCHR |
Vector of chromosomes for each interval. |
iSTART |
Integer vector of the interval start. |
iEND |
Integer vector of the interval end. |
IgnoreBpmapCelPlatformMismatch |
If TRUE, ignores a mismatch between BPMAP and CEL platforms. (EXPERT ONLY!) |
Charles Danko
## Note that executing the following example requires .bpmap and .cel files in the working directory. ## If these files do not, the program will not execute. ## Creates a sample interval of the first 1MB of chromosome 1-3. ## This function will return a single value for each interval. iCHR <- c("chr1", "chr2", "chr3") iSTART <- rep(1, 3) iEND <- iSTART + 1e+06 ## Get the file names in the current working directory. CEL_NAMES <- dir(pattern=".CEL|.cel"); BPMAP <- dir(pattern=".bpmap"); ## If files are found in the current working directory ... start the analysis!! if( (NROW(CEL_NAMES) > 0) & (NROW(BPMAP) > 0) ) { TilingCelFiles2Probesets(CEL_NAMES, BPMAP, outfilename="NormalizedData.tsv", iID=NULL, iCHR=iCHR, iSTART=iSTART, iEND=iEND); }