getResults {macat} | R Documentation

## 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`

### 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.

### Value

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

### Author(s)

MACAT development team

### See Also

`evalScoring`

### Examples

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

[Package macat version 1.18.0 Index]