MLP {MLP} | R Documentation

## This function calculates p-values for each gene set based on row permutations of the gene p values or column permutations of the expression matrix; the p values can be obtained either as individual gene set p values or p values based on smoothing across gene sets of similar size.

### Description

This function calculates p-values for each gene set based on row permutations of the gene p values or column permutations of the expression matrix; the p values can be obtained either as individual gene set p values or p values based on smoothing across gene sets of similar size.

### Usage

    MLP(geneSet, geneStatistic, minGenes = 5, maxGenes = 100,
      rowPermutations = TRUE, nPermutations = 100, smoothPValues = TRUE,
      probabilityVector = c(0.5, 0.9, 0.95, 0.99, 0.999, 0.9999, 0.99999),
      df = 9, addGeneSetDescription = TRUE)

### Arguments

`geneSet` | is the input list of gene sets (components) and gene IDs (character vectors). A gene set can, for example, be a GO category with for each category Entrez Gene identifiers; The getGeneSets function can be used to construct the geneSet argument for different pathway sources.
`geneStatistic` | is either a named numeric vector (if rowPermutations is TRUE) or a numeric matrix of pvalues (if rowPermutations is FALSE). The names of the numeric vector or row names of the matrix should represent the gene IDs.
`minGenes` | minimum number of genes in a gene set for it to be considered (lower threshold for gene set size)
`maxGenes` | maximum number of genes in a gene set for it to be considered (upper threshold for gene set size)
`rowPermutations` | logical indicating whether to use row permutations (TRUE; default) or column permutations (FALSE)
`nPermutations` | is the number of simulations. By default 100 permutations are conducted.
`smoothPValues` | logical indicating whether one wants to calculate smoothed cut-off thresholds (TRUE; default) or not (FALSE).
`probabilityVector` | vector of quantiles at which p values for each gene set are desired
`df` | degrees of freedom for the smooth.spline function used in getSmoothedPValues
`addGeneSetDescription` | logical indicating whether a column with the gene set description be added to the output data frame; defaults to TRUE.

### Value

data frame with four (or five) columns: totalGeneSetSize, testedGeneSetSize, geneSetStatistic and geneSetPValue and (if addDescription is set to TRUE) geneSetDescription; the rows of the data frame are ordered by ascending geneSetPValue.

### References

Raghavan, Nandini et al. (2007). The high-level similarity of some disparate gene expression measures, Bioinformatics, 23, 22, 3032-3038.

### Examples

    if (require(GO.db)){
      pathExampleGeneSet <- system.file("exampleFiles", "exampleGeneSet.rda", package = "MLP")
      pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
      load(pathExampleGeneSet)
      load(pathExamplePValues)
      head(examplePValues)
      head(exampleGeneSet)
      mlpResult <- MLP(geneSet = exampleGeneSet, geneStatistic = examplePValues)
      head(mlpResult)
    }

[Package MLP version 1.30.0 Index]