summaryStats-methods: Summary statistic per element

In staRank: Stability Ranking

Description

Calculates the summary statistic per element for the whole dataset.

Arguments

data	a matrix with one row per element or a list containing one vector per element.
method	the score that is calculated per gene, one of 'mean' (default), 'median', 'mwtest' (two-sample one sided Mann-Whitney test), 'ttest'(two-sample one sided t-test), 'RSA' (redundant siRNA activity).
decreasing	a boolean indicating the direction of the ranking.

Value

a named vector of the scored elements.

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.