cosineSim: Compute cosine similarities or distances between pairs of...
In PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Description Usage Arguments Value Author(s) References See Also Examples

This function compute cosine similarities or distances between pairs of genes, given measured rich phenotypes.

1 2	cosineSim(x) cosineDist(x)

`x`	a numeric matrix of rich phenotypes with rows and columns specifying samples and genes, respectively.

This function will return either a numeric matrix of cosine similarities or an object of dist.

Xin Wang xw264@cam.ac.uk

Xin Wang, Mauro Castro, Klaas W. Mulder and Florian Markowetz, Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, in preparation.

PANR:assoScore

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toydata<-matrix(rnorm(n=2000, mean=0, sd=4), nrow=100, ncol=20)
toycossim<-cosineSim(t(toydata))
toycosdist<-cosineDist(t(toydata))

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union