Returns information from a BPMAP file for select probes in an Affymetrix tiling array.

Description

parseBPMAP takes as input the path to an Affymetrix BPMAP file, and data on any genomic intervals of particular interest to the analysis.

Returns a matrix, where rows represent each probe on the tiling array and columns representing the following information: "UniqueID" – A unique ID for each probeset of the form: "Chromosome-Start" (if makeUniqueID == TRUE) "CHR" – Chromosome on which the probe is located "Start" – Genomic position in the BPMAP file "PMX" – X index of the spot on the tiling array "PMY" – Y index of the spot on the tiling array "SEQ" – Sequence of the probe (if readProbeSeq == TRUE) "iID" – The ID of the interval in which this probe is located (if an interval was passed)

Note that passing a region of interest returns only probes in that genomic region. If no region is specified, information is returned for all probes on the tiling array.

Usage

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parseBPMAP(filename, iID=NULL, iCHR=NULL, iSTART=NULL, iEND=NULL, recordIntervalIDs = FALSE, makeUniqueID = TRUE, readOnlyNCBI = TRUE, seqIndices = NULL, readProbeSeq = TRUE, verbose = 0)

Arguments

filename

The path to the BPMAP file which describes the arrays specified in the cel files.

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.

recordIntervalIDs

If TRUE, returns a column of the interval ID corresponding to each probe. Requires use of interval data.

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.

seqIndices

If specified, reads only given portions of the BPMAP file (Expert ONLY).

readProbeSeq

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

verbose

if >= 1, returns varying amounts of output in the R window.

Author(s)

Charles Danko

Examples

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## Note that executing the following example requires a .bpmap file in the working directory.
## If one does not exist, the program will not execute.

## Identify a .bpmap file in the current working directory.
BPMAP <- dir(pattern=".bpmap");

## If one or more .bpmap file are present in the current working directory
## returns a list representation of information in the first .bpmap file.
if( NROW(BPMAP) > 0 ) {
  parseBPMAP(BPMAP[0]);
}