setupVars.bgx {bgx}R Documentation

Initialise variables needed to run BGX simulation.

Description

This internal function initialises several variables, which it returns in a list.

Usage

setupVars.bgx(data, samplesets, genes, genesToWatch, probeAff, probecat_threshold, rounding_dec_places = 1)

Arguments

data An AffyBatch object.
samplesets A numeric vector specifying which condition each array belongs to. E.g. if samplesets=c(2,2), then the first two replicates belong to one condition and the last two replicates belong to another condition. If NULL, each array is assumed to belong to a different condition.
genes A numeric vector specifying which genes to analyse. If NULL, all genes are analysed.
genesToWatch A numeric vector specifying which genes to monitor closely amongst those chosen to be analysed (see below for details).
probeAff Stratify the mean (lambda) for the cross-hybridisation parameter (H) by categories according to probe-level sequence information.
probecat_threshold Minimum amount of probes per probe affinity category.
rounding_dec_places The initial probe categorisation is done by rounding affinities to the nearest rounding_dec_places decimal places. 1 is a good value.

Value

A list:

pm Perfect Match probes.
mm MisMatch probes.
samplesets A numeric vector specifying which condition each array belongs to. E.g. if samplesets=c(2,2), then the first two replicates belong to one condition and the last two replicates belong to another condition. If NULL, each array is assumed to belong to a different condition.
probesets A numeric vector specifying how probes are grouped into probesets.
numberOfCategories Number of probe affinity categories.
categories A numeric vector specifying which category each probe belongs to.
unknownProbeSeqs A numeric vector specifying which probes lack sequence information.
numberOfUnknownProbeSeqs Number of probes lacking sequence information.
genesToWatch A numeric vector specifying which genes to monitor closely.
firstProbeInEachGeneToWatch The starting position for each probe in each gene to monitor closely.
numArrays Number of arrays.

Note

This function shouldn't be called directly.

Author(s)

Ernest Turro

References

See bgx

See Also

bgx


[Package bgx version 1.6.0 Index]