parseBPMAP: Returns information from a BPMAP file for select probes in an...
In AffyTiling: Easy extraction of individual probes in Affymetrix tiling arrays

Description Usage Arguments Author(s) Examples

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.

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

`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.

Charles Danko

## 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]);
}