clusterSim: Similarity score between clusters of genes based on pathways...

In BioCor: Functional similarities

Description

Looks for the similarity between genes in groups

Usage

clusterSim(cluster1, cluster2, info, method = "max", ...)

## S4 method for signature 'character,character,GeneSetCollection'
clusterSim(cluster1, cluster2, info, method = "max", ...)

Arguments

cluster1, cluster2	A vector with genes.
info	A GeneSetCollection or a list of genes and the pathways they are involved.
method	one of c("avg", "max", "rcmax", "rcmax.avg", "BMA", "reciprocal"), see Details.
...	Other arguments passed to combineScores

Details

Once the pathways for each cluster are found they are combined using combineScores.

Value

clusterSim returns a similarity score of the two clusters

Methods (by class)

• cluster1 = character,cluster2 = character,info = GeneSetCollection: Calculates all the similarities of the GeneSetCollection and combine them using combineScoresPar

Author(s)

Llu<c3><ad>s Revilla

See Also

For a different approach see clusterGeneSim, combineScores and conversions

Examples

if (require("org.Hs.eg.db")) {
    #Extract the paths of all genes of org.Hs.eg.db from KEGG (last update in
    # data of June 31st 2011)
    genes.kegg <- as.list(org.Hs.egPATH)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg, NULL)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg, "avg")
} else {
    warning('You need org.Hs.eg.db package for this example')
}

Example output

If you use BioCor in published research, please cite:
Loading required package: org.Hs.eg.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':

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

[1] 0.07083146

BioCor documentation built on Nov. 8, 2020, 4:56 p.m.