pathSim: Calculates the Dice similarity between pathways

In BioCor: Functional similarities

Description

Calculates the similarity between pathways using dice similarity score. diceSim is used to calculate similarities between the two pathways.

Usage

pathSim(pathway1, pathway2, info)

## S4 method for signature 'character,character,GeneSetCollection'
pathSim(pathway1, pathway2, info)

Arguments

pathway1, pathway2	A single pathway to calculate the similarity
info	A GeneSetCollection or a list of genes and the pathways they are involved.

Value

The similarity between those pathways or all the similarities between each comparison.

Methods (by class)

• pathway1 = character,pathway2 = character,info = GeneSetCollection: Calculates all the similarities of a GeneSetCollection and combine them using combineScoresPar

Author(s)

Llu<c3><ad>s Revilla

See Also

conversions help page to transform Dice score to Jaccard score. mpathSim for multiple pairwise comparison of pathways.

Examples

if (require("reactome.db")){
    # Extracts the paths of all genes of org.Hs.eg.db from reactome
    genes.react <- as.list(reactomeEXTID2PATHID)
    (paths <- sample(unique(unlist(genes.react)), 2))
    pathSim(paths[1], paths[2], genes.react)
} else {
    warning('You need reactome.db package for this example')
}

Example output

If you use BioCor in published research, please cite:
Loading required package: reactome.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, cbind, colMeans, colSums, colnames, 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

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