Tests marker class sizes

Description

Tests if the marker class sizes are large enough for the parameter optimisation scheme, i.e. the size is greater that xval + n, where the default xval is 5 and n is 2. If the test is unsuccessful, a warning is thrown.

Usage

testMarkers(object, xval = 5, n = 2, fcol = "markers", error = FALSE)

Arguments

Details

In case the test indicates that a class contains too few examples, it is advised to either add some or, if not possible, to remove the class altogether (see minMarkers) as the parameter optimisation is likely to fail or, at least, produce unreliable results for that class.

Value

If successfull, the test invisibly returns NULL. Else, it invisibly returns the names of the classes that have too few examples.

Author(s)

Laurent Gatto

See Also

getMarkers and minMarkers

Examples

library("pRolocdata")
data(dunkley2006)
getMarkers(dunkley2006)
testMarkers(dunkley2006)
toosmall <- testMarkers(dunkley2006, xval = 15)
toosmall
try(testMarkers(dunkley2006, xval = 15, error = TRUE))

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(pRoloc)
Loading required package: MSnbase
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: Biobase
Welcome to Bioconductor

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

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
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: XML
Loading required package: cluster

This is pRoloc version 1.12.4 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRoloc/testMarkers.Rd_%03d_medium.png", width=480, height=480)
> ### Name: testMarkers
> ### Title: Tests marker class sizes
> ### Aliases: testMarkers
> 
> ### ** Examples
> 
> library("pRolocdata")

This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> data(dunkley2006)
> getMarkers(dunkley2006)
organelleMarkers
     ER lumen   ER membrane         Golgi Mitochondrion            PM 
           14            45            28            55            46 
      Plastid      Ribosome           TGN       unknown       vacuole 
           20            19            13           428            21 
> testMarkers(dunkley2006)
> toosmall <- testMarkers(dunkley2006, xval = 15)
Warning message:
In testMarkers(dunkley2006, xval = 15) :
  ER lumen, TGN have/has less than 17 markers.
> toosmall
[1] "ER lumen" "TGN"     
> try(testMarkers(dunkley2006, xval = 15, error = TRUE))
Error in testMarkers(dunkley2006, xval = 15, error = TRUE) : 
  ER lumen, TGN have/has less than 17 markers.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>