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aroma.affymetrix (version 2.5.0)

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

## S3 method for class 'default':
bpmapCluster2Cdf(pathname, chipType, tags=NULL, maxProbeDistance=3000, minNbrOfProbes=30, ..., rows=NULL, cols=NULL, groupName=gsub("_.*", "", chipType), field="fullname", stringRemove=sprintf("%s:.*;", groupName), verbose=-10)

Arguments

pathname
The pathname to the BPMAP file.
chipType, tags
The chip type and optional tags of the CDF to be written.
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
minNbrOfProbes
A positive integer specifying the minimum number of probes required in a CDF unit. If fewer, those probes are dropped.
...
Not used.
rows, cols
Two (optional) positive integers. If NULL, optimal values are inferred auotmatically.
groupName
A character string.
field
A character string.
stringRemove
An (optional) regular expression.
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.