gcrma.compute.affinities.local.pmonly: Probe Affinity computation

In jotsetung/generalgcrma: GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.

Description

Compute probe affinities based on their sequence.

Usage

gcrma.compute.affinities.local.pmonly(sequence, verbose = TRUE, affinity.spline.coefs = NULL, pmonly = TRUE, mc.cores )

Arguments

sequence	A character vector with the sequences of the individual probes.
verbose	Plot messages about the progress of the function.
affinity.spline.coefs	Affinity spline coefficients (pre-calculated).
pmonly	Currently only TRUE is supported.
mc.cores	Number of cores (CPUs) on which the affinity computations should be performed. Requires that the multicore package is installed.

Details

See documentation of the compute.affinities.local function in the gcrma package.

Value

A matrix with the same number of columns than affinity.spline.coefs (or only one column if affinity.spline.coefs is a vector) containing the affinity scores for the individual probes.

Author(s)

Johannes Rainer

References

Rainer J, Lelong J, Bindreither D, Mantinger C, Ploner C, Geley S, Kofler R. (2012) Research resource: transcriptional response to glucocorticoids in childhood acute lymphoblastic leukemia. Mol Endocrinol. 2012 Jan;26(1):178-93.

http://bioinfo.i-med.ac.at

Examples

data( "test.sequences" )
data( "affinity.spline.coefs.exon" )
test.sequences[ 1:4 ]

affinity.info <- gcrma.compute.affinities.local.pmonly( sequence=test.sequences, affinity.spline.coefs=affinity.spline.coefs.exon )

affinity.info[ 1:4 ]

jotsetung/generalgcrma documentation built on May 19, 2019, 9:41 p.m.