genes1d {made4} | R Documentation

## genes1d: list top N variables on one axis. Lists the maximum and minimum values in a column of a data.frame

### Description

Lists the top N variables from the positive and negative ends of an axis. Returns a list of N variables that have the max and min. Given a \$co or \$li file it will return that variables at the ends of the axis.

### Usage

    genes1d(array, n = 5, axis = 1, listgenes = FALSE)

### Arguments

`array` | A `matrix` or `data.frame`. Typically a \$co or \$li from `bga`, `cia` or `dudi`.
`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)
`listgenes` | A logical, If TRUE a list containing the variables at each ends of the axes are returned
`...` | further arguments passed to or from other methods

### Details

Genes1d is similar to `link[made4:genes]{genes}`, but returns an index of genes at the ends of one axes.

### Value

Returns a vector or list of vectors.

### Author(s)

Aedin Culhane

### See Also

See Also as `genes`

### Examples

    data(khan)
    if (require(ade4, quiet = TRUE)) {
    khan.coa<-ord(khan$train)
    }
    ind<-topgenes(khan.coa, ends="pos")
    ind.ID<-topgenes(khan.coa, ends="pos", labels=khan$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$ord$co[ind,], row.names=c(1:length(ind)))
    Top10.pos

[Package made4 version 1.66.0 Index]