Identifies outliers in a similarity matrix.

Description

By default uses the Fisher z-transform for Pearson correlation (atanh), and identifies outliers as those above the quantile of a skew-t distribution with mean and standard deviation estimated from the z-transformed matrix. The quantile is calculated from the Bonferroni-corrected cumulative probability of the upper tail.

Usage

outlierFinder(similarity.mat, bonf.prob = 0.05, transFun = atanh,
    normal.upper.thresh = NULL, tail = "upper")

Arguments

Value

Returns either NULL or a dataframe with three columns: sample1, sample2, and similarity.

Author(s)

Levi Waldron, Markus Riester, Marcel Ramos

Examples

library(curatedOvarianData)
data(GSE32063_eset)
cormat <- cor(exprs(GSE32063_eset))
outlierFinder(cormat, bonf.prob = 0.05)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(doppelgangR)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/doppelgangR/outlierFinder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: outlierFinder
> ### Title: Identifies outliers in a similarity matrix.
> ### Aliases: outlierFinder
> 
> ### ** Examples
> 
> library(curatedOvarianData)
Loading required package: affy
> data(GSE32063_eset)
> cormat <- cor(exprs(GSE32063_eset))
> outlierFinder(cormat, bonf.prob = 0.05)
$outlierFinder.res
       sample1   sample2 similarity doppel
2    GSM795126 GSM795125  0.9293563  FALSE
3    GSM795127 GSM795125  0.9325676  FALSE
4    GSM795128 GSM795125  0.9332052  FALSE
5    GSM795129 GSM795125  0.9302175  FALSE
6    GSM795130 GSM795125  0.8833773  FALSE
7    GSM795131 GSM795125  0.9130236  FALSE
8    GSM795132 GSM795125  0.9245368  FALSE
9    GSM795133 GSM795125  0.9235778  FALSE
10   GSM795134 GSM795125  0.9130420  FALSE
11   GSM795135 GSM795125  0.9110784  FALSE
12   GSM795136 GSM795125  0.9164525  FALSE
13   GSM795137 GSM795125  0.9352866  FALSE
14   GSM795138 GSM795125  0.9264104  FALSE
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16   GSM795140 GSM795125  0.8929941  FALSE
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18   GSM795142 GSM795125  0.8998160  FALSE
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41   GSM795125 GSM795126  0.9293563  FALSE
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88   GSM795132 GSM795127  0.9245555  FALSE
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90   GSM795134 GSM795127  0.9170316  FALSE
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94   GSM795138 GSM795127  0.9113129  FALSE
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111  GSM795155 GSM795127  0.9313320  FALSE
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113  GSM795157 GSM795127  0.8952882  FALSE
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117  GSM795161 GSM795127  0.9108426  FALSE
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119  GSM795163 GSM795127  0.8829187  FALSE
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144  GSM795148 GSM795128  0.8825232  FALSE
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146  GSM795150 GSM795128  0.9014635  FALSE
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152  GSM795156 GSM795128  0.9256423  FALSE
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157  GSM795161 GSM795128  0.9102453  FALSE
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160  GSM795164 GSM795128  0.8876021  FALSE
161  GSM795125 GSM795129  0.9302175  FALSE
162  GSM795126 GSM795129  0.9303128  FALSE
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166  GSM795130 GSM795129  0.8779214  FALSE
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168  GSM795132 GSM795129  0.9246801  FALSE
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195  GSM795159 GSM795129  0.9377974  FALSE
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217  GSM795141 GSM795130  0.8801964  FALSE
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219  GSM795143 GSM795130  0.8987083  FALSE
220  GSM795144 GSM795130  0.8951043  FALSE
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225  GSM795149 GSM795130  0.8709530  FALSE
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228  GSM795152 GSM795130  0.9067336  FALSE
229  GSM795153 GSM795130  0.8958714  FALSE
230  GSM795154 GSM795130  0.9088360  FALSE
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233  GSM795157 GSM795130  0.8856275  FALSE
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239  GSM795163 GSM795130  0.8405871  FALSE
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241  GSM795125 GSM795131  0.9130236  FALSE
242  GSM795126 GSM795131  0.9072345  FALSE
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244  GSM795128 GSM795131  0.9233095  FALSE
245  GSM795129 GSM795131  0.9232969  FALSE
246  GSM795130 GSM795131  0.8929946  FALSE
248  GSM795132 GSM795131  0.9282610  FALSE
249  GSM795133 GSM795131  0.9133024  FALSE
250  GSM795134 GSM795131  0.9389506  FALSE
251  GSM795135 GSM795131  0.9269167  FALSE
252  GSM795136 GSM795131  0.9345070  FALSE
253  GSM795137 GSM795131  0.9417357  FALSE
254  GSM795138 GSM795131  0.9107090  FALSE
255  GSM795139 GSM795131  0.9364040  FALSE
256  GSM795140 GSM795131  0.9045136  FALSE
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260  GSM795144 GSM795131  0.9131742  FALSE
261  GSM795145 GSM795131  0.9024670  FALSE
262  GSM795146 GSM795131  0.9377107  FALSE
263  GSM795147 GSM795131  0.9342484  FALSE
264  GSM795148 GSM795131  0.8910238  FALSE
265  GSM795149 GSM795131  0.8744051  FALSE
266  GSM795150 GSM795131  0.9034907  FALSE
267  GSM795151 GSM795131  0.9225847  FALSE
268  GSM795152 GSM795131  0.9337675  FALSE
269  GSM795153 GSM795131  0.9253800  FALSE
270  GSM795154 GSM795131  0.9129663  FALSE
271  GSM795155 GSM795131  0.9253041  FALSE
272  GSM795156 GSM795131  0.9339586  FALSE
273  GSM795157 GSM795131  0.8878492  FALSE
274  GSM795158 GSM795131  0.9208954  FALSE
275  GSM795159 GSM795131  0.9295500  FALSE
276  GSM795160 GSM795131  0.9233666  FALSE
277  GSM795161 GSM795131  0.9091775  FALSE
278  GSM795162 GSM795131  0.9076860  FALSE
279  GSM795163 GSM795131  0.8846687  FALSE
280  GSM795164 GSM795131  0.8722287  FALSE
281  GSM795125 GSM795132  0.9245368  FALSE
282  GSM795126 GSM795132  0.9219239  FALSE
283  GSM795127 GSM795132  0.9245555  FALSE
284  GSM795128 GSM795132  0.9229844  FALSE
285  GSM795129 GSM795132  0.9246801  FALSE
286  GSM795130 GSM795132  0.8992055  FALSE
287  GSM795131 GSM795132  0.9282610  FALSE
289  GSM795133 GSM795132  0.9265361  FALSE
290  GSM795134 GSM795132  0.9313326  FALSE
291  GSM795135 GSM795132  0.9308772  FALSE
292  GSM795136 GSM795132  0.9387540  FALSE
293  GSM795137 GSM795132  0.9535337  FALSE
294  GSM795138 GSM795132  0.9340485  FALSE
295  GSM795139 GSM795132  0.9468003  FALSE
296  GSM795140 GSM795132  0.9237310  FALSE
297  GSM795141 GSM795132  0.9185987  FALSE
298  GSM795142 GSM795132  0.9402575  FALSE
299  GSM795143 GSM795132  0.9479899  FALSE
300  GSM795144 GSM795132  0.9193319  FALSE
301  GSM795145 GSM795132  0.9180568  FALSE
302  GSM795146 GSM795132  0.9446770  FALSE
303  GSM795147 GSM795132  0.9394773  FALSE
304  GSM795148 GSM795132  0.9183651  FALSE
305  GSM795149 GSM795132  0.8995292  FALSE
306  GSM795150 GSM795132  0.9035325  FALSE
307  GSM795151 GSM795132  0.9407350  FALSE
308  GSM795152 GSM795132  0.9377225  FALSE
309  GSM795153 GSM795132  0.9307952  FALSE
310  GSM795154 GSM795132  0.9362639  FALSE
311  GSM795155 GSM795132  0.9383226  FALSE
312  GSM795156 GSM795132  0.9412168  FALSE
313  GSM795157 GSM795132  0.9144101  FALSE
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315  GSM795159 GSM795132  0.9473217  FALSE
316  GSM795160 GSM795132  0.9315808  FALSE
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318  GSM795162 GSM795132  0.9350201  FALSE
319  GSM795163 GSM795132  0.8994433  FALSE
320  GSM795164 GSM795132  0.8982400  FALSE
321  GSM795125 GSM795133  0.9235778  FALSE
322  GSM795126 GSM795133  0.9151077  FALSE
323  GSM795127 GSM795133  0.9172230  FALSE
324  GSM795128 GSM795133  0.9078128  FALSE
325  GSM795129 GSM795133  0.9226156  FALSE
326  GSM795130 GSM795133  0.8932922  FALSE
327  GSM795131 GSM795133  0.9133024  FALSE
328  GSM795132 GSM795133  0.9265361  FALSE
330  GSM795134 GSM795133  0.9167504  FALSE
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