MCtest: Monte Carlo permutation test

Description Usage Arguments Value Author(s) References See Also Examples

Description

This function performs Monte Carlo permutation test to asses the statistical significance of R and Q statistics.

Usage

1
MCtest(RAN, RQ, nper = 100)

Arguments

RAN

matrix of ranks to be permuted, columns refer to studies, rows refer to genes

RQ

observed values of R (average rank) and Q (heterogenity) - as produced by compute.RQ

nper

number of permutations

Value

Returns a matrix with four columns. First (Second) column represents significance level of high (low) avarage rank. Third (fourth) represents significance level of high (low) heterogenity.

Author(s)

Ivana Ihnatova

References

Zintzaras, E., Ioannidis, J.P.A 2008 Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays, Computational Biology and Chemistry 32, 39-47

See Also

rank.genes,compute.RQ

Examples

1
2
3
4
RANK<-cbind(sample(100), sample(100), sample(100))
RQ<-compute.RQ(RANK)
head(RQ)       
MCtest(RANK, RQ, nper=100)

Example output

Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

The following object is masked from 'package:genefilter':

    rowVars

Loading required package: xtable
Loading required package: multtest
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, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

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

    multExpFDR, zScoreFDR, zScorePermuted, zScores

       r.star      q.star
[1,] 72.33333  928.666667
[2,] 48.33333 3980.666667
[3,] 52.00000 3614.000000
[4,] 21.33333  650.666667
[5,] 75.66667  752.666667
[6,] 33.66667    4.666667
100          R.high R.low Q.high Q.low
  [1,]   0.13  0.87   0.62  0.38
  [2,]   0.67  0.33   0.07  0.93
  [3,]   0.45  0.56   0.09  0.91
  [4,]   0.94  0.06   0.70  0.30
  [5,]   0.05  0.95   0.71  0.29
  [6,]   0.82  0.18   1.00  0.00
  [7,]   0.23  0.77   0.35  0.65
  [8,]   0.13  0.88   0.56  0.44
  [9,]   0.73  0.27   0.45  0.55
 [10,]   1.00  0.00   0.97  0.04
 [11,]   0.79  0.23   0.40  0.60
 [12,]   0.50  0.50   0.07  0.93
 [13,]   0.55  0.47   0.98  0.02
 [14,]   0.54  0.46   0.15  0.85
 [15,]   0.32  0.69   0.11  0.89
 [16,]   0.04  0.96   0.70  0.30
 [17,]   0.30  0.70   0.75  0.25
 [18,]   0.35  0.65   0.06  0.94
 [19,]   0.54  0.47   0.99  0.01
 [20,]   0.01  0.99   0.97  0.03
 [21,]   0.78  0.23   0.45  0.55
 [22,]   0.36  0.65   0.14  0.86
 [23,]   0.30  0.71   0.33  0.67
 [24,]   0.31  0.70   0.70  0.30
 [25,]   0.46  0.54   0.32  0.69
 [26,]   0.76  0.24   0.29  0.71
 [27,]   0.24  0.77   0.05  0.95
 [28,]   0.25  0.75   0.04  0.96
 [29,]   0.05  0.95   0.67  0.33
 [30,]   0.40  0.62   0.02  0.98
 [31,]   0.40  0.60   0.25  0.75
 [32,]   0.20  0.81   0.59  0.41
 [33,]   0.87  0.13   0.79  0.21
 [34,]   0.69  0.32   0.01  0.99
 [35,]   0.59  0.42   0.07  0.93
 [36,]   0.90  0.10   1.00  0.00
 [37,]   0.86  0.14   0.47  0.53
 [38,]   0.29  0.72   0.50  0.50
 [39,]   0.70  0.30   0.87  0.13
 [40,]   0.60  0.40   0.06  0.94
 [41,]   0.55  0.45   0.06  0.94
 [42,]   0.81  0.20   0.91  0.09
 [43,]   0.21  0.79   0.90  0.10
 [44,]   0.99  0.01   0.61  0.39
 [45,]   0.04  0.96   0.52  0.48
 [46,]   0.17  0.83   0.01  0.99
 [47,]   0.14  0.86   0.65  0.35
 [48,]   0.51  0.50   0.79  0.21
 [49,]   0.29  0.71   0.94  0.06
 [50,]   0.61  0.40   0.54  0.46
 [51,]   0.80  0.21   0.98  0.02
 [52,]   0.31  0.69   0.98  0.02
 [53,]   0.13  0.87   0.60  0.40
 [54,]   0.82  0.18   0.15  0.85
 [55,]   0.82  0.18   0.69  0.32
 [56,]   0.80  0.20   0.89  0.11
 [57,]   0.00  1.00   0.99  0.01
 [58,]   0.65  0.35   0.34  0.67
 [59,]   0.75  0.26   0.60  0.41
 [60,]   0.43  0.58   0.45  0.55
 [61,]   0.29  0.71   0.01  0.99
 [62,]   0.92  0.08   0.42  0.58
 [63,]   0.47  0.54   0.67  0.33
 [64,]   0.24  0.78   0.74  0.26
 [65,]   0.87  0.13   0.83  0.17
 [66,]   0.81  0.19   0.46  0.54
 [67,]   0.27  0.74   1.00  0.00
 [68,]   0.85  0.16   0.86  0.14
 [69,]   0.11  0.89   0.18  0.83
 [70,]   0.98  0.02   0.99  0.02
 [71,]   0.80  0.23   0.37  0.63
 [72,]   0.83  0.17   0.49  0.51
 [73,]   0.02  0.98   0.71  0.29
 [74,]   0.61  0.40   0.56  0.44
 [75,]   0.69  0.32   0.99  0.02
 [76,]   0.63  0.37   0.00  1.00
 [77,]   0.18  0.82   0.22  0.78
 [78,]   0.13  0.88   0.47  0.55
 [79,]   0.57  0.44   0.32  0.68
 [80,]   0.23  0.77   0.71  0.29
 [81,]   0.92  0.09   0.80  0.20
 [82,]   0.03  0.97   0.81  0.19
 [83,]   0.93  0.08   0.39  0.61
 [84,]   0.77  0.23   0.16  0.84
 [85,]   0.97  0.03   0.71  0.29
 [86,]   0.91  0.09   0.56  0.44
 [87,]   0.15  0.85   0.37  0.63
 [88,]   0.71  0.29   0.18  0.82
 [89,]   0.77  0.23   0.18  0.82
 [90,]   0.58  0.42   0.38  0.62
 [91,]   0.61  0.39   0.10  0.90
 [92,]   0.09  0.91   0.42  0.58
 [93,]   0.65  0.35   0.15  0.85
 [94,]   0.40  0.60   0.67  0.33
 [95,]   0.88  0.13   0.37  0.63
 [96,]   0.06  0.95   0.73  0.27
 [97,]   0.18  0.84   0.82  0.18
 [98,]   0.31  0.70   0.18  0.82
 [99,]   0.50  0.51   0.53  0.47
[100,]   0.16  0.85   0.75  0.25
Warning message:
system call failed: Cannot allocate memory 

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.

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