Description Usage Arguments Details Value Author(s) References See Also Examples
The function wilcox.selection.split
performs variable ordering based on the Wilcoxon rank sum test for all niter
CV or MCCV iterations.
1 | wilcox.selection.split(x,y,split,algo="new",pvalue=FALSE)
|
x |
a matrix or a data frame of size n x p giving the expression levels of the p variables (genes) for the n observations (arrays). Variables correspond to columns, observations to rows. |
y |
a vector of length n giving the class membership for the n observations (arrays). |
split |
A |
algo |
either |
pvalue |
Logical. Should p-values be returned? |
The Wilcoxon rank sum statistic is defined as the sum of the X-ranks of
the observations with y=0
. The Wilcoxon rank sum test is equivalent to the
Mann-Whitney test. It is implemented in the function wilcox.test
.
In the context of cross-validation (CV) or Monte-Carlo cross-validation (MCCV), wilcox.selection.split
computes the
Wilcoxon rank sum statistic for each iteration, for each variable. At each iteration, a subset
of the n
observations is excluded from the data set and considered as test data set.
The indices of the observations considered as test set for each of the niter
iterations
are given in the niter
x ntest
matrix split
.
A list with the following components:
ordering.split |
A |
pvalue.split |
Returned only if |
Anne-Laure Boulesteix (http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/index.html)
A. L. Boulesteix (2007). WilcoxCV: an R package for fast variable selection in cross-validation. Bioinformatics 23:1702-1704.
wilcox.test
, generate.split
, generate.cv
, wilcox.split
1 2 3 4 5 6 7 8 9 10 11 12 | # load WilcoxCV library
library(WilcoxCV)
# Generate data
x<-matrix(rnorm(1000),100,10)
y<-sample(c(0,1),100,replace=TRUE)
# Generate 50 MCCV splits with ratio 2:1 for a data set including 90 observations
my.split<-generate.split(niter=50,n=90,ntest=30)
# Compute the Wilcoxon rank sum statistic for the 50 iterations.
wilcox.selection.split(x=x,y=y,split=my.split,algo="new",pvalue=TRUE)
|
$ordering.split
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 4 9 3 8 6 10 2 5 1
[2,] 9 4 5 10 3 6 1 7 2 8
[3,] 10 6 4 7 3 5 9 1 8 2
[4,] 4 7 6 5 3 10 2 1 8 9
[5,] 8 6 9 5 7 4 3 2 1 10
[6,] 10 9 4 2 7 3 5 6 8 1
[7,] 4 9 10 7 2 8 5 6 3 1
[8,] 4 5 3 9 2 10 6 7 8 1
[9,] 4 10 5 9 1 7 6 2 8 3
[10,] 9 4 7 1 10 2 5 8 3 6
[11,] 4 10 7 8 5 3 2 6 9 1
[12,] 10 9 6 4 1 3 7 8 5 2
[13,] 4 7 1 9 3 10 6 2 5 8
[14,] 10 9 3 2 5 4 8 1 7 6
[15,] 10 4 9 1 3 6 8 5 2 7
[16,] 7 10 4 3 6 1 5 8 9 2
[17,] 4 7 1 9 5 3 2 6 10 8
[18,] 3 10 4 6 8 9 5 2 7 1
[19,] 7 1 9 10 4 5 3 2 6 8
[20,] 4 10 3 2 5 1 7 9 8 6
[21,] 3 7 4 9 1 6 8 2 10 5
[22,] 4 7 8 10 9 5 2 1 6 3
[23,] 4 9 7 8 10 1 2 5 3 6
[24,] 4 9 3 2 7 6 1 8 10 5
[25,] 4 6 5 8 7 10 2 1 9 3
[26,] 4 9 7 6 2 3 8 5 1 10
[27,] 4 9 1 6 3 7 5 10 8 2
[28,] 7 4 3 1 5 10 9 8 6 2
[29,] 9 1 4 10 5 6 2 7 3 8
[30,] 4 9 3 10 7 5 8 1 6 2
[31,] 4 2 1 9 6 10 5 3 7 8
[32,] 9 4 5 6 1 7 3 8 10 2
[33,] 4 2 3 10 9 5 7 6 1 8
[34,] 9 4 8 6 3 7 10 2 5 1
[35,] 7 3 10 8 6 9 4 1 2 5
[36,] 4 3 10 9 5 6 7 2 8 1
[37,] 9 4 10 6 1 7 3 2 5 8
[38,] 4 3 9 8 5 1 7 10 6 2
[39,] 9 4 8 6 10 2 1 7 5 3
[40,] 1 9 5 4 7 6 3 8 10 2
[41,] 4 3 8 2 1 7 10 6 9 5
[42,] 10 3 4 1 7 5 8 9 6 2
[43,] 4 10 5 3 9 1 6 7 8 2
[44,] 9 7 3 10 5 4 1 6 8 2
[45,] 4 6 10 2 5 9 8 3 7 1
[46,] 4 6 9 5 3 7 2 1 8 10
[47,] 4 10 9 8 3 7 1 6 2 5
[48,] 9 1 4 5 10 8 3 7 2 6
[49,] 3 10 4 9 2 1 7 5 8 6
[50,] 4 3 9 2 7 1 8 6 5 10
$pvalue.split
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.80446009 0.5957469 0.36398919 0.15371625 0.6972371 0.54766450
[2,] 0.76122660 0.8648785 0.51944230 0.27398412 0.3308589 0.74277552
[3,] 0.75024527 0.9248583 0.49410787 0.13741817 0.5476645 0.10374808
[4,] 0.77676349 0.7675319 0.58301899 0.09003695 0.5665694 0.49542818
[5,] 0.99030210 0.7612266 0.69731006 0.57607874 0.5273539 0.36197337
[6,] 0.90553034 0.4987451 0.62655566 0.20839589 0.7129461 0.77577623
[7,] 0.89715209 0.4662738 0.71565075 0.02635651 0.6808664 0.68086640
[8,] 0.81981899 0.4081276 0.30820015 0.17552002 0.2969564 0.42881087
[9,] 0.57930491 0.7520415 0.95721271 0.06903439 0.2859395 0.70724291
[10,] 0.45617396 0.6207502 0.88152811 0.11416577 0.7340119 0.89094404
[11,] 0.99053107 0.7848841 0.60154227 0.07700998 0.4128553 0.93379213
[12,] 0.46541294 0.9470910 0.49542818 0.31370931 0.8991875 0.27486484
[13,] 0.24417254 0.8918442 0.61531491 0.13168151 0.9011986 0.77206317
[14,] 0.77577623 0.5529196 0.34847186 0.57698958 0.5529196 0.84010992
[15,] 0.54500715 0.9526820 0.62655566 0.13482446 0.8493992 0.80318740
[16,] 0.82915184 0.9235949 0.40136755 0.39467511 0.8478888 0.43583845
[17,] 0.20381392 0.6487096 0.64011079 0.04658448 0.3375263 0.65735546
[18,] 0.99518659 0.8611191 0.09234851 0.29664004 0.8046430 0.57476634
[19,] 0.26385474 0.7902160 0.73613839 0.45277536 0.4527754 0.79021601
[20,] 0.71092992 0.3743894 0.32590089 0.09362902 0.5603086 0.87380141
[21,] 0.55842886 0.8233707 0.17086356 0.21619336 0.9855605 0.72189129
[22,] 0.72724318 0.4891394 0.86387652 0.09201608 0.4599237 0.72724318
[23,] 0.72189129 0.7675319 0.85164867 0.24921618 0.7953203 0.85164867
[24,] 0.95268203 0.5216123 0.19580638 0.03567578 0.9905311 0.70411606
[25,] 0.50054899 0.4855078 0.62919174 0.17221022 0.2700969 0.24505179
[26,] 0.83472516 0.5313570 0.53135702 0.20845216 0.7520415 0.38737500
[27,] 0.17418016 0.8552983 0.57626236 0.12469203 0.6421248 0.44092732
[28,] 0.35560810 0.8268162 0.24821017 0.16585405 0.5844016 0.77981449
[29,] 0.13784688 0.7272432 0.91994717 0.17205786 0.4671347 0.48913936
[30,] 0.78488413 0.8773877 0.24965893 0.02646757 0.5689116 0.83084286
[31,] 0.20839589 0.1613929 0.52161228 0.08105991 0.5063078 0.30742872
[32,] 0.46184960 0.9055303 0.67786844 0.26972028 0.2801550 0.36081045
[33,] 0.71092992 0.2233341 0.29776858 0.15973739 0.5524128 0.58431881
[34,] 0.74864159 0.6015423 0.49124288 0.22608046 0.6692035 0.48380168
[35,] 0.58074845 0.6722719 0.25928386 0.50298485 0.7156507 0.37814643
[36,] 0.89681622 0.7681948 0.16417732 0.13128512 0.3829785 0.53207446
[37,] 0.62883397 0.8596323 0.82275721 0.09644929 0.9623874 0.60394406
[38,] 0.67211151 0.9952436 0.26495245 0.02039811 0.6634358 0.90982080
[39,] 0.57437553 0.4965964 0.87318194 0.23472789 0.7450691 0.44569024
[40,] 0.06425775 0.8825049 0.72724318 0.23941737 0.1954307 0.54258185
[41,] 0.59132649 0.4085280 0.30225941 0.07126387 0.9374894 0.65965411
[42,] 0.42273539 0.9436072 0.24793932 0.37025249 0.5167124 0.77721706
[43,] 0.56499467 0.9235949 0.42881087 0.04928913 0.2806111 0.58131698
[44,] 0.50054899 0.8254289 0.32530560 0.42786401 0.3617277 0.55507797
[45,] 0.91493944 0.2306643 0.63499179 0.01598899 0.2448108 0.09425603
[46,] 0.70956366 0.5270207 0.48913936 0.03690092 0.4671347 0.17205786
[47,] 0.73401186 0.8254289 0.50816119 0.12847833 0.8440445 0.75204154
[48,] 0.25388089 0.7272432 0.62365436 0.26894171 0.4817430 0.73613839
[49,] 0.61531491 0.5347727 0.15084230 0.28996030 0.6920392 0.73613839
[50,] 0.73360435 0.4732913 0.29029755 0.07397659 0.8362973 0.76122660
[,7] [,8] [,9] [,10]
[1,] 0.08101219 0.4866923 0.30504019 0.57950660
[2,] 0.76122660 0.9515391 0.09347117 0.36840957
[3,] 0.48669231 0.7862695 0.56347712 0.09181589
[4,] 0.34974899 0.7953203 0.92789684 0.59968798
[5,] 0.52735388 0.3130467 0.48841964 1.00000000
[6,] 0.55291962 0.8493992 0.14765240 0.11721949
[7,] 0.37182097 0.5888241 0.22167265 0.27966072
[8,] 0.54889601 0.6747845 0.34360000 0.41495512
[9,] 0.69839786 0.9192790 0.47808003 0.14414804
[10,] 0.43484397 0.8254289 0.02313167 0.53920656
[11,] 0.22608046 0.3304733 0.95268203 0.16861531
[12,] 0.59132649 0.7583333 0.11817441 0.07916864
[13,] 0.23941737 0.9387404 0.43171119 0.70078150
[14,] 0.80318740 0.7129461 0.29631523 0.29086056
[15,] 0.99053107 0.8308429 0.18378349 0.04241791
[16,] 0.32558725 0.8572903 0.89508605 0.38805062
[17,] 0.18328713 0.9617535 0.32558725 0.92359488
[18,] 0.94709101 0.5747663 0.79532026 0.16344891
[19,] 0.23010383 0.8825049 0.26385474 0.41122632
[20,] 0.71971317 0.7912255 0.77315518 0.17793877
[21,] 0.17852731 0.7675319 0.48029276 0.84219957
[22,] 0.34723136 0.3472314 0.43171119 0.41122632
[23,] 0.36871670 0.4654129 0.31370931 0.68606987
[24,] 0.52161228 0.9621376 0.10652243 0.97159856
[25,] 0.38737500 0.3371718 0.61235833 0.40731956
[26,] 0.36803758 0.5711743 0.23550485 0.94771681
[27,] 0.60058698 0.7821756 0.17048116 0.75520705
[28,] 0.05635164 0.7153768 0.63547290 0.58440156
[29,] 0.85458994 0.9199472 0.09201608 0.42481805
[30,] 0.37982519 0.5851212 0.09194421 0.29631523
[31,] 0.71294607 0.8031874 0.21272007 0.30742872
[32,] 0.46184960 0.7848841 0.12578216 0.78488413
[33,] 0.56825871 0.9671535 0.53678688 0.51377235
[34,] 0.57698958 0.4196598 0.04122455 0.58512123
[35,] 0.09994413 0.3718210 0.41747400 0.36556156
[36,] 0.64566715 0.8689025 0.33960404 0.23375665
[37,] 0.76819479 0.9717859 0.03909752 0.55554334
[38,] 0.74300908 0.6548050 0.38086143 0.77933879
[39,] 0.72724318 0.3293402 0.13784688 0.44569024
[40,] 0.36572905 0.8084834 0.15768056 0.86387652
[41,] 0.59968798 0.3817106 0.78602668 0.62508755
[42,] 0.48669231 0.6039441 0.62048847 0.18279077
[43,] 0.59785654 0.8950860 0.44293198 0.13090915
[44,] 0.19171470 0.7520415 0.10364512 0.33120435
[45,] 0.76669906 0.3304733 0.30742872 0.11177003
[46,] 0.51169053 0.7630326 0.37202917 0.80848340
[47,] 0.51583368 0.3939561 0.36803758 0.18768919
[48,] 0.64047794 0.5743755 0.12573204 0.48174303
[49,] 0.61531491 0.7272432 0.38482977 0.17580091
[50,] 0.49608047 0.7519833 0.38814185 0.90325686
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