ScorePGSEA {GeneExpressionSignature} | R Documentation

## Compute pairwise distances between samples with method in package PGSEA

### Description

Compute pairwise distances between sample according to their (Prototype Ranked List) PRL, get a `N x N` distance matrix is generated by calling this function , `N` is the length of PRL.

### Usage

    ScorePGSEA(
      MergingSet,
      SignatureLength,
      ScoringDistance = c("avg", "max"),
      p.value = FALSE
    )

### Arguments

`MergingSet` | an `Biobase::ExpressionSet` object. The assay data represents the PRLs of the samples, each column represents one PRL. The number of sample must be greater than 1, otherwise, this function is not meaningful.
`SignatureLength` | the length of "gene signature". In order to compute pairwise distances among samples, genes lists are ranked according to the gene expression ratio (fold change). And the "gene signature" includes the most up-regulated genes (near the top of the list) and the most down-regulated genes (near the bottom of the list).
`ScoringDistance` | the distance measurements between PRLs: the Average Enrichment Score Distance ("avg"), or the Maximum Enrichment Score Distance ("max").
`p.value` | logical, if `TRUE` return a matrix of `p.values` of the distance matrix, default `FALSE`.

### Value

an distance-matrix, the max distance is more sensitive to weak similarities, providing a lower precision but a larger recall.If `p.value` is set to `TRUE`, then a list is returned that consists of the distance matrix as well as their p.values, otherwise, without p.values in the result.

### See Also

`ScoreGSEA()`,`SignatureDistance()`

### Examples

    # load the sample expressionSet
    data(exampleSet)
    # Merging each group of the ranked lists in the exampleSet with the same
    # phenotypic data into a single PRL
    MergingSet <- RankMerging(exampleSet,"Spearman")
    # get the distance matrix
    ds <- ScorePGSEA(MergingSet,250, ScoringDistance="avg")

[Package GeneExpressionSignature version 1.38.0 Index]