filterPmat.RdFilter rows of p-value matrix under the significance threshold
filterPmat(x, threshold)| x | A matrix of p-values. It must be raw p-values and should not be transformed (e.g. logarithmic). |
|---|---|
| threshold | A numeric value, the minimal p-value used to filter
rows. If missing, given the values of |
Matrix of p-values. If no line is left, a empty matrix of the same dimension as input will be returned.
Jitao David Zhang <jitao_david.zhang@roche.com>
set.seed(1235)
testMatrix <- matrix(runif(100,0,1), nrow=10)
## filtering
(testMatrix.filter <- filterPmat(testMatrix, threshold=0.05))
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] 0.09942167 0.519080359 0.8610312 0.7301602 0.02303889 0.29758641
#> [2,] 0.42356115 0.006524904 0.7941721 0.5956656 0.89373905 0.67286840
#> [3,] 0.54449943 0.913918048 0.3366246 0.2526326 0.31682109 0.11527104
#> [4,] 0.21233559 0.846787080 0.4409803 0.1011335 0.11404830 0.06292524
#> [,7] [,8] [,9] [,10]
#> [1,] 0.08470704 0.667210379 0.1024085 0.1629068
#> [2,] 0.47513906 0.866471735 0.8204760 0.2696054
#> [3,] 0.30904022 0.006296073 0.4914639 0.7755592
#> [4,] 0.10296535 0.042746874 0.3686046 0.6102488
## more strict filtering
(testMatrix.strictfilter <- filterPmat(testMatrix, threshold=0.01))
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 0.4235611 0.006524904 0.7941721 0.5956656 0.8937391 0.6728684 0.4751391
#> [2,] 0.5444994 0.913918048 0.3366246 0.2526326 0.3168211 0.1152710 0.3090402
#> [,8] [,9] [,10]
#> [1,] 0.866471735 0.8204760 0.2696054
#> [2,] 0.006296073 0.4914639 0.7755592
## no filtering
(testMatrix.nofilter <- filterPmat(testMatrix))
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] 0.24259237 0.955264658 0.1735149 0.6600869 0.49964633 0.36426726
#> [2,] 0.51535594 0.542894020 0.9506383 0.4464108 0.91183977 0.35510430
#> [3,] 0.09942167 0.519080359 0.8610312 0.7301602 0.02303889 0.29758641
#> [4,] 0.90153593 0.629080697 0.2500496 0.5944550 0.47802527 0.28223439
#> [5,] 0.83890292 0.743721835 0.2265801 0.3249363 0.88662049 0.49429587
#> [6,] 0.42356115 0.006524904 0.7941721 0.5956656 0.89373905 0.67286840
#> [7,] 0.54449943 0.913918048 0.3366246 0.2526326 0.31682109 0.11527104
#> [8,] 0.74531624 0.601582744 0.5318425 0.3366423 0.49811558 0.91560261
#> [9,] 0.54546342 0.656368798 0.2052040 0.6242061 0.71044726 0.59158016
#> [10,] 0.21233559 0.846787080 0.4409803 0.1011335 0.11404830 0.06292524
#> [,7] [,8] [,9] [,10]
#> [1,] 0.09635398 0.845977069 0.5661316 0.54604221
#> [2,] 0.49347185 0.538405826 0.6771958 0.05492638
#> [3,] 0.08470704 0.667210379 0.1024085 0.16290676
#> [4,] 0.64331855 0.120438496 0.3671928 0.36080728
#> [5,] 0.98718476 0.540113622 0.5900340 0.64481398
#> [6,] 0.47513906 0.866471735 0.8204760 0.26960538
#> [7,] 0.30904022 0.006296073 0.4914639 0.77555919
#> [8,] 0.88986665 0.391184572 0.8414607 0.67942271
#> [9,] 0.95679199 0.977328825 0.3580521 0.99959032
#> [10,] 0.10296535 0.042746874 0.3686046 0.61024876