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

Description

AnalyzeTilingCelFiles 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.

By default, preforms background correction, quantile normalization, and log2 transform. This can be disabled by setting ReturnRawIntensities to TRUE, if raw intensity values are desired.

This function returns a matrix, where rows represent probes and columns represent the following values: –Unique probe ID –Probe start position (in genomic coordinates) –Chromosome –Sequence –Intensity for sample 1 –Intensity for sample 2 ... –Intensity for sample N

Usage

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AnalyzeTilingCelFiles(CEL_filenames, BPMAP_filename, outfilename=NULL, iID=NULL, iCHR=NULL, iSTART=NULL, iEND=NULL, makeUniqueID=TRUE, readOnlyNCBI=TRUE, readProbeSeq=FALSE, IgnoreBpmapCelPlatformMismatch=FALSE, ReturnRawIntensities=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.

iCHR

Vector of chromosomes for each interval.

iSTART

Integer vector of the interval start.

iEND

Integer vector of the interval end.

makeUniqueID

If TRUE (default), returns a column of unique identifiers for each probe, of the form: chr-start.

readOnlyNCBI

If TRUE (default), returns ONLY probes that target NCBI sequences, TIGR and Affymetrix controls are ignored.

readProbeSeq

If TRUE, returns the first 25 bp of the probe sequence.

IgnoreBpmapCelPlatformMismatch

If TRUE, ignores a mismatch between BPMAP and CEL platforms. (EXPERT ONLY!)

ReturnRawIntensities

If TRUE, returns raw intensity values associated with the specified regions. Otherwise (default) preforms RMA-like processing of data using the affy package. Processing includes background correction, quantile normalization, and a log-2 transform.

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.

## 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) ) {
  AnalyzeTilingCelFiles(CEL_NAMES, BPMAP, outfilename="NormalizedData.tsv");
}