setupVars.bgx {bgx} | R Documentation |
This internal function initialises several variables, which it returns in a list.
setupVars.bgx(data, samplesets, genes, genesToWatch, probeAff, probecat_threshold, rounding_dec_places = 1)
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. |
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. |
This function shouldn't be called directly.
Ernest Turro
See bgx