geneSetGPS {chroGPS} | R Documentation

## Highlight point (gene) position over a Multi-dimensional Scaling plot.

### Description

Given a list of genes of interest, the function highlights their position over a Multi-dimensional Scaling plot.

### Usage

    geneSetGPS(x, m, genes, uniqueCount = TRUE, ...)

### Arguments

`x` | Matrix or data frame of observations x variables (tipically genes x epigenetic factors), with gene identifiers as rownames.
`m` | Object of class `mds` with a valid Multidimensional Scaling representation for the elements in `x`.
`genes` | Character vector containing gene identifiers, matching those on rownames(x).
`uniqueCount` | Set to FALSE if the MDS has been generated directly from the data in `x`, otherwise set to TRUE to match gene identifiers with their unique pattern of observed variables.
`...` | Additional parameters given to the generic function `plot`.

### Value

Matrix with coordinates on the given input MDS object for the genes selected.

### Author(s)

Oscar Reina

### Examples

    # Not run
    # data(s2)
    # d <- distGPS(s2.tab,metric='tanimoto',uniqueRows=TRUE)
    # mds1 <- mds(d)
    # set.seed(149)
    # sampleGenes <- rownames(s2.tab)[sample(1:nrow(s2.tab),10,rep=FALSE)]
    # pts <- geneSetGPS(s2.tab,mds1,genes=sampleGenes,uniqueCount=TRUE)
    # plot(mds1)
    # points(getPoints(pts),col='red',cex=3)

[Package chroGPS version 1.28.0 Index]