bpmapCluster2Cdf: Creates a CDF from tiling-array BPMAP file
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

bpmapCluster2Cdf

R Documentation

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

## Default S3 method:
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 `integer`s 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/<chipType>/`.
`verbose`	See `Verbose`.

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").