aroma.affymetrix (version 3.0.0)

bpmapCluster2Cdf: Creates a CDF from tiling-array BPMAP file

Description

Creates a CDF from tiling-array BPMAP file.

NOTE: This method applies only to Affymetrix tiling arrays! Furthermore, it is likely to be more useful for promoter tiling arrays and less so for whole-genome tiling arrays.

Usage

"bpmapCluster2Cdf"(pathname, chipType, tags=NULL, rows, cols, maxProbeDistance=3000L, minNbrOfProbes=30L, groupName=gsub("_.*", "", chipType), field="fullname", stringRemove=sprintf("%s:.*;", groupName), ..., flavor=c("v2", "v1"), path="*", verbose=-10)

Arguments

pathname

The pathname to the BPMAP file.

chipType, tags

The chip type and optional tags of the CDF to be written.

rows, cols

Two positive integers specifying the probe dimension of the chip. It is important to get this correct. They can be inferred from the CEL header of a CEL file for this chip, cf. readCelHeader.

maxProbeDistance

A positive integer specifying the maximum genomic distance (in basepairs) allowed between two probes in order to "cluster" those two probes into the same CDF units. Whenever the distance is greater, the two probes end up in two different CDF units.

minNbrOfProbes

A positive integer specifying the minimum number of probes required in a CDF unit. If fewer, those probes are dropped.

groupName

A character string specifying which BPMAP sequences to keep. Sequence with this group name is kept, all others are excluded.

field

A character string.

stringRemove

An (optional) regular expression.

...

Optional arguments passed to readBpmap.

flavor

Specifying which version of BPMAP-to-CDF generator to use. The default is always to use the most recent one, which is also the recommended one. Previous versions are kept only for backward compatibility (and may be dropped at anytime).

path

The directory where the CDF file will be written. If "*" (default), it will be written to annotationData/chipTypes//.

verbose

See Verbose.

Value

Returns (invisibly) a the pathname of the created CDF file. The created CDF is written to the current directory.

Details

This method applies only to Affymetrix tiling arrays. It is likely to be useful for promoter tiling arrays and less so for whole-genome tiling arrays. Flavor "v2" replaced "v1" as aroma.affymetrix v2.5.4 (June 21, 2012). For details, see news(package="aroma.affymetrix").