findSimilar: findSimilar

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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)

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.