Similarity score genes based on pathways similarity

Given two genes, calculates the Dice similarity between each pathway which is combined to obtain a similarity between the genes.

Usage

mgeneSim(genes, info, method = "max", ...)

# S4 method for class 'character,GeneSetCollection'
mgeneSim(genes, info, method = "max", ...)

# S4 method for class 'missing,GeneSetCollection'
mgeneSim(genes, info, method = "max", ...)

Arguments

genes

A vector of 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

Value

mgeneSim returns the matrix of similarities between the genes in the vector

Details

Given the information about the genes and their pathways, uses the ids of the genes to find the Dice similarity score for each pathway comparison between the genes. Later this similarities are combined using combineScoresPar().

Methods (by class)

• mgeneSim(genes = character, info = GeneSetCollection): Calculates all the similarities of the list and combine them using combineScoresPar()

• mgeneSim(genes = missing, info = GeneSetCollection): Calculates all the similarities of the list and combine them using combineScoresPar()

Note

genes accept named characters and the output will use the names of the genes.

See also

geneSim(), conversions() help page to transform Dice score to Jaccard score. For the method to combine the scores see combineScoresPar().

Examples

if (require("org.Hs.eg.db") & require("reactome.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)
    # Extracts the paths of all genes of org.Hs.eg.db from reactome
    genes.react <- as.list(reactomeEXTID2PATHID)
    mgeneSim(c("81", "18", "10"), genes.react)
    mgeneSim(c("81", "18", "10"), genes.react, "avg")
    named_genes <- structure(c("81", "18", "10"),
        .Names = c("ACTN4", "ABAT", "NAT2")
    )
    mgeneSim(named_genes, genes.react, "max")
} else {
    warning("You need reactome.db and org.Hs.eg.db package for this example")
}
#>            ACTN4       ABAT       NAT2
#> ACTN4 1.00000000 0.12133072 0.05482166
#> ABAT  0.12133072 1.00000000 0.05124605
#> NAT2  0.05482166 0.05124605 1.00000000