pickBestFromDupGroup

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

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")]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(RefNet)
Loading required package: IRanges
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RefNet/pickBestFromDupGroup.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pickBestFromDupGroup
> ### Title: pickBestFromDupGroup
> ### Aliases: pickBestFromDupGroup
> ### Keywords: utilities
> 
> ### ** 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")]
  A.common B.common                                 type provider
1     PTEN     TP53 psi-mi:MI:0915(physical association)  BioGrid
    publicationID
1 pubmed:12620407
> 
>       # 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)
[1] 6
>     tbl.dups[bestOfDups, c("A.common", "B.common", "type", "provider", "publicationID")]
   A.common B.common                                 type  provider
5       RB1     TP53 psi-mi:MI:0915(physical association)   BioGrid
15      TXN     TP53   psi-mi:MI:0407(direct interaction)   BioGrid
1      PTEN     TP53 psi-mi:MI:0915(physical association)   BioGrid
9      EGFR   PIK3R1   psi-mi:MI:0407(direct interaction)   BioGrid
12   PIK3R1   PIK3CA   psi-mi:MI:0407(direct interaction)   BioGrid
54      RB1   PIK3R1          psi-mi:MI:0191(aggregation) iRefIndex
     publicationID
5  pubmed:20871633
15 pubmed:19681600
1  pubmed:12620407
9  pubmed:16273093
12  pubmed:7929193
54 pubmed:15657099
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>