topgenes {made4} | R Documentation

## Topgenes, returns a list of variables at the ends (positive, negative or both) of an axis

### Description

`topgenes` will return a list of the top N variables from the positive, negative or both ends of an axis. That is, it returns a list of variables that have the maximum and/or minimum values in a vector.

### Usage

    topgenes(x, n = 10, axis = 1, labels = row.names(x), ends = "both", ...)

### Arguments

`x` | A `vector`, `matrix` or `data.frame`. Typically a data frame \$co or \$li from `dudi` or \$ls, \$li, \$co from `bga`.
`n` | An integer indicating the number of variables to be returned. Default is 5.
`axis` | An integer indicating the column of x. Default is 1 (first axis, of \$co or \$li file)
`labels` | A vector of row names, for x[,axis]. Default values is row.names(x)
`ends` | A string, "both", "neg", "pos", indicating whether variable label should be return from both, the negative or the positive end of an axis. The default is both.
`...` | further arguments passed to or from other methods

### Details

`topgenes` calls `genes1d`. `genes1d` is similar to `genes`, but returns an index of genes at the ends of one axis not two axes. Given a \$co or \$li file it will return that variables at the ends of the axis.

### Value

Returns a vector or list of vectors.

### Author(s)

AedinCulhane

### See Also

See Also as `genes`

### Examples

    # Simple example
    a<-rnorm(50)
    order(a)
    topgenes(a, labels=c(1:length(a)), ends="neg")

    # Applied example
    data(khan)
    if (require(ade4, quiet = TRUE)) {
    khan.coa<-ord(khan$train[1:100,])}
    ind<-topgenes(khan.coa, ends="pos")
    ind.ID<-topgenes(khan.coa, ends="pos", labels=khan$gene.labels.imagesID)
    ind.symbol<-topgenes(khan.coa, ends="pos", labels=khan$annotation$Symbol)
    Top10.pos<- cbind("Gene Symbol"=ind.symbol,
          "Clone ID"=ind.ID, "Coordinates"=khan.coa$ord$li[ind,], row.names=c(1:length(ind)))
    Top10.pos

[Package made4 version 1.68.0 Index]