get_results: Access results of 'evalScoring'
In macat: MicroArray Chromosome Analysis Tool

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	getResults(MACATevalScoringOBJ)

MACATevalScoringOBJ

Object of class MACATevalScoring, usually the result from evalScoring

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.

A list with the following components, describing probe sets within chromosome regions deemed significant:

`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

MACAT development team

evalScoring

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