Calculate the labeling efficiency of isobaric labeling data

Description

Calculate the labeling efficiency of isobaric labeling data

Usage

labelRatio(ms = NULL, iClass = 1, delta = 0.05, plot = TRUE)

Arguments

Value

A vector object

Author(s)

Bo Wen wenbo@genomics.cn

Examples

mgf.zip <- system.file("extdata/mgf.zip", package = "proteoQC")
unzip(mgf.zip)
a <- labelRatio("test.mgf")

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)

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> library(proteoQC)
Loading required package: XML
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/proteoQC/labelRatio.Rd_%03d_medium.png", width=480, height=480)
> ### Name: labelRatio
> ### Title: Calculate the labeling efficiency of isobaric labeling data
> ### Aliases: labelRatio
> 
> ### ** Examples
> 
> mgf.zip <- system.file("extdata/mgf.zip", package = "proteoQC")
> unzip(mgf.zip)
> a <- labelRatio("test.mgf")
1000
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>