summary {staRank} | R Documentation

## Summary method for RankSummary object

### Description

This function summarizes the top 10 elements for each of the three ranking types 'stability', 'base', 'averaged'. It also contains their (spearman) rank correlation coefficients and stability information about the top 1,10 and 50

### Arguments

`object` | a RankSummary object.

### Value

a summary of a 'RankSummary' object.

### 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 1.30.0 Index]