summary-methods: Summary method for RankSummary object

In staRank: Stability Ranking

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)

Example output

Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
   a    h    d    g    i    c    e    f    j    b 
3.75 4.00 4.25 4.25 4.25 5.00 6.00 6.25 8.50 8.75 
  h   a   d   c   g   i   e   f   j   b 
3.0 3.5 4.0 4.5 4.5 5.0 6.0 6.5 8.5 9.0 
   a    b    c    d    e    f    g    h    i    j 
3.75 8.75 5.00 4.25 6.00 6.25 4.25 4.00 4.25 8.50 
          a           b           c           d           e           f 
-1.01371011 -0.09275405 -0.52306887 -1.65233426 -0.34896305 -0.40683372 
          g           h           i           j 
-0.93452887 -1.00000000 -1.09668435 -0.05281597 
  a   g   i   c   h   d   e   f   b   j 
1.0 2.5 2.5 4.5 4.5 6.5 6.5 8.0 9.5 9.5 
     Length       Class        Mode 
          1 RankSummary          S4 
  mean_stability mean_base mean_averaged
a            1.0         1             1
g            2.5         4             3
i            2.5         4             2
c            4.5         6             6
h            4.5         2             4
d            6.5         4             5
e            6.5         7             7
f            8.0         8             8
b            9.5        10            10
j            9.5         9             9

staRank documentation built on Nov. 8, 2020, 7:51 p.m.