computeAffinities.AffymetrixCdfFile {aroma.affymetrix}R Documentation

Calculates probe affinities from sequence

Description

Calculates probe affinities from sequence.

Adapted from compute.affinities in the gcrma package. Attempts to find the tab-separated probe sequence file associated with a particular CDF, and matches sequence to probe index in order to assign an affinity to each probe.

Usage

## S3 method for class 'AffymetrixCdfFile':
computeAffinities(this, paths=NULL, safe=TRUE, force=FALSE, verbose=FALSE, ...)

Arguments

paths A character variable containing location(s) to look for the probe sequence file. Multiple locations should be separated by semi-colons.
force If FALSE, cached results is returned, if available.
verbose See Verbose.
... Not used.

Value

Returns a numeric vector of (log2) probe affinities, of length equal to the total number of features on the array.

Author(s)

Ken Simpson (ksimpson[at]wehi.edu.au).


[Package aroma.affymetrix version 1.2.0 Index]