pickBestFromDupGroup: pickBestFromDupGroup

In RefNet: A queryable collection of molecular interactions, from many sources

Description

Assign a shared "dupGroup" number to each duplicated interaction, here defined as A.canonical, type, B.canonical. All other information about the interaction is ignored. An A-B interaction is treated the same as a B-A interaction. This assessment prepares a possibly large interaction set for scrutiny by eye, or programmatically, for filtering, in which a single preferred interaction can be selected, out of each dupGroup, for further use.

Note that preferred.interaction.types elements may be substrings of the full (and often unwieldy) interaction type names used in the underlying data.

Usage

  pickBestFromDupGroup(dupGrp, tbl.dups,
                       preferred.interaction.types)

Arguments

dupGrp	an integer
tbl.dups	data.frame, returned by detectDuplicateInteractions.
preferred.interaction.types	list of character strings

Value

The row name (or names, for dupGroup 0) of the tbl.dups row which is the best match to the ordered list of preferred.interaction.types.

Author(s)

Paul Shannon

See Also

RefNet, providerClasses, interactions, addStandardNames, detectDuplicateInteractions

Examples

    filename <- system.file(package="RefNet", "extdata", "tbl.dups.RData")
    load(filename)
    preferred.types <- c("direct", "physical", "aggregation")

      # get the best from dupGroup 1
    best.1 <- pickBestFromDupGroup(1, tbl.dups, preferred.types)
    tbl.dups[best.1, c("A.common", "B.common", "type", "provider", "publicationID")]

      # get all of the best.  not every dupGroup will pass muster
    dupGroups <- sort(unique(tbl.dups$dupGroup))
    bestOfDups <- unlist(lapply(dupGroups, function(dupGroup) 
                       pickBestFromDupGroup(dupGroup, tbl.dups, preferred.types)))
    deleters <- which(is.na(bestOfDups))
    if(length(deleters) > 0)
        bestOfDups <- bestOfDups[-deleters]
    length(bestOfDups)
    tbl.dups[bestOfDups, c("A.common", "B.common", "type", "provider", "publicationID")]

RefNet documentation built on April 29, 2020, 4:12 a.m.