Subset IBSpectra objects

Description

Returns an IBSpectra object which is a subset of the input, excluding or exclusively containing the peptides or proteins supplied.

Usage

subsetIBSpectra(x, protein = NULL, peptide = NULL,
                direction = "exclude",
                specificity = c(REPORTERSPECIFIC, GROUPSPECIFIC, UNSPECIFIC), ...)

Arguments

Author(s)

Florian P Breitwieser

See Also

protein.g, spectrumSel, specificities

Examples

data(ibspiked_set1)

# get Keratin proteins
keratin.proteins <- protein.g(proteinGroup(ibspiked_set1),"Keratin")

# exclude Keratin proteins
subsetIBSpectra(ibspiked_set1,protein=keratin.proteins,direction="exclude")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(isobar)
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")'.

Welcome to isobar (v 1.18.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

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

    normalize

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

    paste0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isobar/subsetIBSpectra.Rd_%03d_medium.png", width=480, height=480)
> ### Name: subsetIBSpectra
> ### Title: Subset IBSpectra objects
> ### Aliases: subsetIBSpectra
> 
> ### ** Examples
> 
> data(ibspiked_set1)
> 
> # get Keratin proteins
> keratin.proteins <- protein.g(proteinGroup(ibspiked_set1),"Keratin")
> 
> # exclude Keratin proteins
> subsetIBSpectra(ibspiked_set1,protein=keratin.proteins,direction="exclude")
Creating ProteinGroup ... done
iTRAQ4plexSpectra (storageMode: lockedEnvironment)
assayData: 14801 features, 4 samples 
  element names: ions, mass 
protocolData: none
phenoData: none
featureData
  featureNames: M261-D07-HS-P1948-1.1765.1765.2.dta.38373
    M261-C07-HS-P1948-1.2376.2376.3.dta.26320 ...
    M261-D06-HS-P1948-1.1660.1660.3.dta.37304 (14801 total)
  fvarLabels: peptide modif ... use.for.quant (12 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
14801  spectra
ProteinGroup object
    1574 peptides are detected
     150 protein groups with specific peptides
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>