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 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 usingcombineScoresPar()
See also
mgeneSim(), 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)
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