getResults: Access results of 'evalScoring'

Description

This function processes the result of the evalScoring function and returns a list of probe sets within chromosome regions deemed significant by MACAT. Additional annotation for these probe sets is provided along with their identifiers.

Usage

getResults(MACATevalScoringOBJ)

Arguments

MACATevalScoringOBJ

Object of class MACATevalScoring, usually the result from evalScoring

Value

probeID: IDs of probe sets within these chromosome regions
cytoband: chromosomal bands these probe sets have been annotated to
geneSYM: gene symbols these probe sets have been annotated to
pvalue: p-values for probe sets; see details
locusid: EntrezGene-(formerly LocusLink) IDs of these probe sets
genedescription: Description of genes the probe sets have been annotated to
probeScore: the differential expression scores for the probe sets
chromosome: chromosome, the analysis has been done for
class: sample class, the analysis has been done for

Details

The p-values have been computed individually for probe sets (genes), not for whole chromosome regions. Thus, regions deemed significant by sliding window approach do not have to consist only of probe sets with low p-values. These probe-set p-values are not used to determine whether a region is considered significant or not. Instead the comparison between actual and interpolated scores to actual and interpolated boundaries determines whether a region is considered significant.

This function is called within the plot function for the results of evalScoring, when HTML output is desired.

Examples

Run this code

data(stjd)
myevalres <- evalScoring(stjd, class="T", chromosome=6, nperms=10,
                         cross.validate=FALSE) 
results <- getResults(myevalres)
summary(results)
results$probeID[1:20]