Extract a stratified sample of an MSnSet

Description

This function extracts a stratified sample of an MSnSet.

Usage

sampleMSnSet(object, fcol = "markers", size = 0.2, seed)

Arguments

Value

A stratified sample (according to the defined fcol) which is an instance of class "MSnSet".

Author(s)

Lisa Breckels

See Also

testMSnSet unknownMSnSet markerMSnSet. See markers for details about markers encoding.

Examples

library(pRolocdata)
data(tan2009r1)
dim(tan2009r1)
smp <- sampleMSnSet(tan2009r1, fcol = "markers")
dim(smp)
getMarkers(tan2009r1)
getMarkers(smp)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/sampleMSnSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sampleMSnSet
> ### Title: Extract a stratified sample of an 'MSnSet'
> ### Aliases: sampleMSnSet
> 
> ### ** Examples
> 
> library(pRolocdata)

This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> data(tan2009r1)
> dim(tan2009r1)
[1] 888   4
> smp <- sampleMSnSet(tan2009r1, fcol = "markers")
Warning message:
New sample contains classes with < 6 markers 
> dim(smp)
[1] 182   4
> getMarkers(tan2009r1)
organelleMarkers
 Cytoskeleton            ER         Golgi      Lysosome       Nucleus 
            7            28            13             8            21 
           PM    Peroxisome    Proteasome  Ribosome 40S  Ribosome 60S 
           34             4            15            20            32 
mitochondrion       unknown 
           29           677 
> getMarkers(smp)
organelleMarkers
 Cytoskeleton            ER         Golgi      Lysosome       Nucleus 
            2             6             3             2             5 
           PM    Peroxisome    Proteasome  Ribosome 40S  Ribosome 60S 
            7             1             3             4             7 
mitochondrion       unknown 
            6           136 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>