detectDuplicateInteractions

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.

Usage

  detectDuplicateInteractions(tbl)

Arguments

Value

A data.frame identical to the one passed as an argument, but with one additional column "dupGroup". dupGroup 0 (zero) contains all of the interactions which have NO duplicates.

Author(s)

Paul Shannon

See Also

RefNet, providerClasses, interactions, addStandardNames, pickBestFromDupGroup

Examples

  filename <- system.file(package="RefNet", "extdata", "tbl.28g2.RData")
  load(filename)
  tbl.withDupsColumn <- detectDuplicateInteractions(tbl.28g2)
  table(tbl.withDupsColumn$dupGroup)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/detectDuplicateInteractions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: detectDuplicateInteractions
> ### Title: detectDuplicateInteractions
> ### Aliases: detectDuplicateInteractions
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   filename <- system.file(package="RefNet", "extdata", "tbl.28g2.RData")
>   load(filename)
>   tbl.withDupsColumn <- detectDuplicateInteractions(tbl.28g2)
>   table(tbl.withDupsColumn$dupGroup)

 0  1  2  3  4  5  6  7  8 
 5 11  8 10 16  3  5  2  2 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>