setupVars.bgx: Initialise variables needed to run BGX simulation.

In bgx: Bayesian Gene eXpression

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

bgx documentation built on Nov. 8, 2020, 5:57 p.m.