staRank (version 1.14.0)

summary: 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)