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

geneSim(gene1, gene2, info, method = "max", ...)

# S4 method for class 'character,character,GeneSetCollection'
geneSim(gene1, gene2, info, method = "max", ...)

Arguments

gene1, gene2

Ids of the genes to calculate the similarity, to be found in 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

The highest Dice score of all the combinations of pathways between the two ids compared if a method to combine scores is provided or NA if there isn't information for one gene. If an NA is returned this means that there isn't information available for any pathways for one of the genes. Otherwise a number between 0 and 1 (both included) is returned. Note that there isn't a negative value of similarity.

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)

• geneSim(gene1 = character, gene2 = character, info = GeneSetCollection): Calculates all the similarities of the GeneSetCollection and combine them using combineScoresPar()

See also

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

Author

Lluís Revilla

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)
    geneSim("81", "18", genes.react)
    geneSim("81", "18", genes.kegg)
    geneSim("81", "18", genes.react, NULL)
    geneSim("81", "18", genes.kegg, NULL)
} else {
    warning("You need reactome.db and org.Hs.eg.db package for this example")
}
#> Loading required package: reactome.db
#>       00250 00280 00410 00640 00650       01100
#> 04510     0     0     0     0     0 0.001503759
#> 04520     0     0     0     0     0 0.000000000
#> 04530     0     0     0     0     0 0.000000000
#> 04670     0     0     0     0     0 0.003210273
#> 04810     0     0     0     0     0 0.004467610
#> 05146     0     0     0     0     0 0.011326861
#> 05322     0     0     0     0     0 0.000000000
#> 05412     0     0     0     0     0 0.000000000