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

View source: R/wilcox_score-methods.R

This test evaluates whether the mean rank of statistics of gene set members is greater or less than the mean rank of the remaining statistic values. It extends the rankSumTestWithCorrelation function from the 'limma' package by taking into account the 'sign' of gene set members by reversing the ranks of down-regulated genes.

1 2 |

`statistics` |
numeric vector giving values of the test statistic. |

`index.up` |
an index vector such that statistics[index.up] contains the values of the statistic for the up-regulated genes. |

`index.down` |
an index vector such that statistics[index.down] contains the values of the statistic for the down-regulated genes. |

`correlation` |
numeric scalar, average correlation between cases in the test group. Cases in the second group are assumed independent of each other and the first group. |

`df` |
degrees of freedom which the correlation has been estimated. |

`adjust.ties` |
logical: correct for ties ? |

`input.is.ranks` |
logical: is 'statistics' a vector of ranks ? If FALSE (default), ranks are computed. If FALSE, 'statistics' is assumed to represent ranks and is used directly. |

Please see the rankSumTestWithCorrelation function from the limma package for details.

Numeric vector containing U-statistic, z-score and p-value.

Thomas Sandmann

Wu, D, and Smyth, GK (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Submitted.

Barry, W.T., Nobel, A.B., and Wright, F.A. (2008). A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2, 286-315.

Zar, JH (1999). Biostatistical Analysis 4th Edition. Prentice-Hall International, Upper Saddle River, New Jersey.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
genes.up <- c(1:10)
genes.down <- c(21:30)
set.seed(123)
scores <- matrix(rnorm(200), ncol=2)
## the first gene set receives increased /
## decreased scores in the first experiment
scores[genes.up,1] <- scores[genes.up ,1] + 1
scores[genes.down,1] <- scores[genes.down,1] - 1
## significantly greater
signedRankSumTest( statistics = scores[,1],
index.up = genes.up,
index.down = genes.down)
## not signficant
signedRankSumTest( statistics = scores[,2],
index.up = genes.up,
index.down = genes.down)
``` |

```
Loading required package: GSEABase
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, 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,
rowMeans, rowSums, 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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Attaching package: 'gCMAP'
The following object is masked from 'package:IRanges':
members
U p z
1.890000e+02 7.169693e-08 5.260846e+00
U p z
874.0000000 0.2632461 -0.6333697
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.