getStability: getStability
In staRank: Stability Ranking

Description Usage Arguments Value Examples

Performes stability selection on sample rankings with a given stability threshold. Selection probabilities and stability ranking are calculated.

1	getStability(sr, thr, Pi = FALSE, verbose = FALSE)

`sr`	sample rankings in the form of a matrix where each row corresponds to one element and each column gives one ranking.
`thr`	the threshold for the stability selection, indicating above which frequency in the samples an element is considered stable.
`Pi`	boolean indicating if the Pi matrix should be returned (can be very large, default=FALSE).
`verbose`	boolean indicating whether status updates should be printed

a list containing:

stabRank: the stable ranking.
Pi: the frequency matrix with all values per gene and per cutoff.
stableSetSize: a table with the number of stable genes per cutoff.

# 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)

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   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