getStability {staRank} | R Documentation

## getStability

### Description

Performes stability selection on sample rankings with a given stability threshold. Selection probabilities and stability ranking are calculated.

### Usage

      getStability(sr, thr, Pi = FALSE, verbose = FALSE)

### Arguments

`sr` | sample rankings in the form of a matrix where each row corresponds to one element and each column gives one ranking.
`thr` | the threshold for the stability selection, indicating above which frequency in the samples an element is considered stable.
`Pi` | boolean indicating if the Pi matrix should be returned (can be very large, default=FALSE).
`verbose` | boolean indicating whether status updates should be printed

### Value

a list containing:

`stabRank`

  the stable ranking.

`Pi`

  the frequency matrix with all values per gene and per cutoff.

`stableSetSize`

  a table with the number of stable genes per cutoff.

### Examples

    # generate dataset
    d<-replicate(4,sample(1:10,10,replace=FALSE))
    rownames(d)<-letters[1:10]

    # rank aggregation on the dataset using two base methods
    aggregRank(d, method='mean')
    aggregRank(d, method='median')

    # calculate summary statistic from the data
    summaryStats(d, method='mean')
    summaryStats(d, method='RSA')

    # calculating replicate scores from different summary statistics
    scores<-getSampleScores(d,'mean',decreasing=FALSE,bootstrap=TRUE)
    scores<-getSampleScores(d,'mwtest',decreasing=FALSE,bootstrap=TRUE)

    # perform RSA analysis

    # get RSA format of data
    rsaData<-dataFormatRSA(d)
    # set RSA options
    opts<-list(LB=min(d),UB=max(d),reverse=FALSE)
    # run the RSA analysis
    r<-runRSA(rsaData,opts)
    # directly obtain the per gene RSA ranking from the data
    r<-uniqueRSARanking(rsaData,opts)

    # get stable Ranking, stable setsizes and the Pi matrix for default settings
    # and stability threshold of 0.9
    s<-getStability(d,0.9)

    # run default stability ranking
    s<-stabilityRanking(d)

    # using an accessor function on the RankSummary object
    stabRank(s)

    # summarize a RankSummary object
    summary(s)

    # generate a rank matrix from a RankSummary object
    getRankmatrix(s)

[Package staRank version 1.34.0 Index]