Background correction and RNA normalization for CEL files from an Affymetrix tiling array.

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Description

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.

Usage

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TilingCelFiles2Probesets(CEL_filenames, BPMAP_filename, outfilename=NULL, iID=NULL, iCHR, iSTART, iEND, IgnoreBpmapCelPlatformMismatch=FALSE)

Arguments

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!)

Author(s)

Charles Danko

Examples

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## 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);
}