Find genes that are not connected to the others.

Description

A function that takes as input a distance matrix and finds those entries that are not connected to any others (ie. those with distance Inf.

Usage

notConn(dists)

Arguments

Details

It is a very naive implementation. It presumes that not connected entries are not connected to any other entries, and this might not be true. Using the connComp function from the graph package or the RBGL package might be a better approach.

Value

A vector of the names of the items that are not connected.

Author(s)

R. Gentleman

See Also

connComp

Examples

 data(Ndists)
 notConn(Ndists)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GOstats)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand

Loading required package: graph


Attaching package: 'GOstats'

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

    makeGOGraph

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GOstats/notConn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: notConn
> ### Title: Find genes that are not connected to the others.
> ### Aliases: notConn
> ### Keywords: manip
> 
> ### ** Examples
> 
>  data(Ndists)
>  notConn(Ndists)
[1] "32025_at" "35705_at" "35940_at" "37280_at" "39143_at" "506_s_at"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>