dataFormatRSA {staRank} | R Documentation

## dataFormatRSA

### Description

Creates a data.frame in the RSA input format from a matrix, where rows indicate the genes and columns the replicate or siRNA values.

### Usage

      dataFormatRSA(dataMatrix)

### Arguments

`dataMatrix` | a matrix with one row per gene and columns are replicate or siRNA values.

### Value

a data.frame with three columns Gene_ID, Well_ID, Score. The Well_ID does not have a meaning if data are replicates, but is usefull to distinguish between siRNAs.

### 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]