getLeadingEdgeIndexFromVector {BioQC} | R Documentation

## Getting leading-edge indices from a vector

### Description

Getting leading-edge indices from a vector

### Usage

    getLeadingEdgeIndexFromVector(
      x,
      index,
      comparison = c("greater", "less"),
      reference = c("background", "geneset")
    )

    getLeadingEdgeIndexFromMatrix(
      x,
      index,
      comparison = c("greater", "less"),
      reference = c("background", "geneset")
    )

### Arguments

`x` | A numeric vector (`getLeadingEdgeIndexFromVector`) or a numeric matrix (`getLeadingEdgeIndexFromMatrix`).
`index` | An integer vector, indicating the indices of genes in a gene-set.
`comparison` | Character string, are values greater than or less than the reference value considered as leading-edge? This depends on the type of value requested by the user in `wmwTest`.
`reference` | Character string, which reference is used? If `background`, genes with expression higher than the median of the background are reported. Otherwise in the case of `geneset`, genes with expression higher than the median of the gene-set is reported. Default is `background`, which is consistent with the results of the Wilcoxon-Mann-Whitney tests.

### Value

An integer vector, indicating the indices of leading-edge genes.

### Functions

- `getLeadingEdgeIndexFromMatrix`: `x` is a `matrix`.

### See Also

`wmwTest`

### Examples

    myProfile <- c(rnorm(5, 3), rnorm(15, -3), rnorm(100, 0))
    getLeadingEdgeIndexFromVector(myProfile, 1:20)
    getLeadingEdgeIndexFromVector(myProfile, 1:20, comparison="less")
    getLeadingEdgeIndexFromVector(myProfile, 1:20, comparison="less", reference="geneset")
    myProfile2 <- c(rnorm(15, 3), rnorm(5, -3), rnorm(100, 0))
    myProfileMat <- cbind(myProfile, myProfile2)
    getLeadingEdgeIndexFromMatrix(myProfileMat, 1:20)
    getLeadingEdgeIndexFromMatrix(myProfileMat, 1:20, comparison="less")
    getLeadingEdgeIndexFromMatrix(myProfileMat, 1:20, comparison="less", reference="geneset")

[Package BioQC version 1.22.0 Index]