Removes non-identified features

Description

The method removes non-identifed features in MSnExp and MSnSet instances using relevant information from the feaureData slot of a user-provide filtering vector of logicals.

Methods

signature(object = "MSnExp", fcol = "pepseq", keep = NULL)

Removes the feature from object that have a feature fcol (default is "pepseq") equal to NA. Alternatively, one can also manually define keep, a vector of logical, defining the feature to be retained.

signature(object = "MSnSet", fcol = "pepseq", keep = NULL)

As above of MSnSet instances.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

See Also

MSnExp and MSnSet.

Examples

  quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "mzXML$")
  identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "dummyiTRAQ.mzid")
  msexp <- readMSData(quantFile)
  msexp <- addIdentificationData(msexp, identFile)
  fData(msexp)$pepseq
  length(msexp)

  ## using default fcol
  msexp2 <- removeNoId(msexp)
  length(msexp2)
  fData(msexp2)$pepseq

  ## using keep
  print(fvarLabels(msexp))
  (k <- fData(msexp)$'ms-gf:evalue' > 75)
  k[is.na(k)] <- FALSE
  k
  msexp3 <- removeNoId(msexp, keep = k)
  length(msexp3)
  fData(msexp3)$pepseq

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(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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/removeNoId-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: removeNoId-methods
> ### Title: Removes non-identified features
> ### Aliases: removeNoId-methods removeNoId
> ### Keywords: methods
> 
> ### ** Examples
> 
>   quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
+                      full.name = TRUE, pattern = "mzXML$")
>   identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
+                      full.name = TRUE, pattern = "dummyiTRAQ.mzid")
>   msexp <- readMSData(quantFile)
Reading 5 MS2 spectra from file dummyiTRAQ.mzXML
   |                                                                               |                                                                      |   0%   |                                                                               |==============                                                        |  20%   |                                                                               |============================                                          |  40%   |                                                                               |==========================================                            |  60%   |                                                                               |========================================================              |  80%   |                                                                               |======================================================================| 100%
Caching...
Creating 'MSnExp' object
>   msexp <- addIdentificationData(msexp, identFile)
reading dummyiTRAQ.mzid... DONE!
>   fData(msexp)$pepseq
[1] "VESITARHGEVLQLRPK" "IDGQWVTHQWLKK"     NA                 
[4] NA                  "LVILLFR"          
>   length(msexp)
[1] 5
> 
>   ## using default fcol
>   msexp2 <- removeNoId(msexp)
>   length(msexp2)
[1] 3
>   fData(msexp2)$pepseq
[1] "VESITARHGEVLQLRPK" "IDGQWVTHQWLKK"     "LVILLFR"          
> 
>   ## using keep
>   print(fvarLabels(msexp))
 [1] "spectrum"                  "scan number(s)"           
 [3] "passthreshold"             "rank"                     
 [5] "calculatedmasstocharge"    "experimentalmasstocharge" 
 [7] "chargestate"               "ms-gf:denovoscore"        
 [9] "ms-gf:evalue"              "ms-gf:rawscore"           
[11] "ms-gf:specevalue"          "assumeddissociationmethod"
[13] "isotopeerror"              "isdecoy"                  
[15] "post"                      "pre"                      
[17] "end"                       "start"                    
[19] "accession"                 "length"                   
[21] "description"               "pepseq"                   
[23] "modified"                  "modification"             
[25] "idFile"                    "databaseFile"             
[27] "nprot"                     "npep.prot"                
[29] "npsm.prot"                 "npsm.pep"                 
>   (k <- fData(msexp)$'ms-gf:evalue' > 75)
[1]  TRUE FALSE    NA    NA  TRUE
>   k[is.na(k)] <- FALSE
>   k
[1]  TRUE FALSE FALSE FALSE  TRUE
>   msexp3 <- removeNoId(msexp, keep = k)
>   length(msexp3)
[1] 2
>   fData(msexp3)$pepseq
[1] "VESITARHGEVLQLRPK" "LVILLFR"          
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>