findSimilar {cummeRbund} | R Documentation

## findSimilar

### Description

Returns a CuffGeneSet containing n genes with the most similar expression profiles to gene/profile x.

### Usage

    ## S4 method for signature 'CuffSet'
    findSimilar(object, x, n,distThresh,returnGeneSet=TRUE,...)

### Arguments

`object` | A object of class 'CuffSet'
`x` | A 'gene_id' or 'gene_short_name' from which to look up an expression profile OR a vector of expression values to compare all genes (vector must have same length and order of 'samples')
`n` | Number of similar genes to return
`distThresh` | A thresholding value on which to filter results based on JS-distance (e.g. A distThresh of 1.0 will return all genes, 0.0 will return those genes with 'perfect identity' to the gene of interest.)
`returnGeneSet` | A logical value whether to return a CuffGeneSet object [default] or a distance-ranked data frame of similar genes. The latter is useful if you want to explore the returned list based on distances.
`...` | Additional arguments to fpkmMatrix call within findSimilar (e.g. fullnames=T)

### Details

By default, returns a CuffGeneSet object with n similar genes. This may change in the future.

### Value

A CuffGeneSet object of n most similar genes to x.

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### Examples

    	a<-readCufflinks(system.file("extdata", package="cummeRbund"))
    	mySimilarGenes<-findSimilar(a,"PINK1",10)

[Package cummeRbund version 2.28.0 Index]