hyperG: Hypergeometric test

In SLGI: Synthetic Lethal Genetic Interaction

Description

a hypergeometric test for genetic interaction data.

Usage

hyperG(data, nbTested, universe)

Arguments

data	Matrix with 2 columns the first one corresponds to the number of interactions per pair of interacting complexes and the second one to number of tested interactions. This could be the first two columns resulting from a call to the test2Interact function.
nbTested	Number of interacting pairs
universe	Total Number of tested pairs

Author(s)

N. LeMeur

See Also

phyper

Examples

## Create matrix interaction x tested matrix
interact <-  c(1, 3, 2, 2, 6, 5, 2, 4, 1, 3)
tested <-  c(3, 3, 5, 4, 8, 5, 3, 4, 2, 3)
mat <- cbind(interact, tested)

## Perform test
res <- hyperG(mat, 1000, 10000)
summary(res$P)

Example output

Loading required package: ScISI
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid


Loading required package: RpsiXML
Loading required package: annotate
Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode

Loading required package: RBGL
Loading required package: hypergraph
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’

Attaching package: ‘RpsiXML’

The following object is masked from ‘package:IRanges’:

    members

Loading required package: apComplex

Loading required package: lattice
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
9.910e-06 3.239e-04 1.449e-02 6.248e-02 7.413e-02 2.710e-01 

SLGI documentation built on Nov. 8, 2020, 11 p.m.