R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Match a GC-MS pseudospectrum to a database with a weighted...

matchExpSpec

R Documentation

Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.

Description

Function matchExpSpec calculates match factors for a pseudospectrum with all entries in the database. A plot of the best match can be provided. Function mzmatch is an auxiliary function, not meant to be called directly, that provides the match factor, given two appropriately scaled patterns.

Usage

matchExpSpec(pspec, DB, DB.treated, plotIt = FALSE,
             scale.p = c("sqrt", "none"), mass.weight = TRUE, ...)
mzmatch(spec1, spec2)

Arguments

`pspec`	The pseudospectrum, a two- or three-column matrix where the third column (the retention time) will be ignored.
`DB`	Database of standards.
`DB.treated`	Logical, indicating whether the database has already been scaled (TRUE) or not.
`plotIt`	Logical: show best match?
`scale.p`	indicates whether `"sqrt"` scaling or no scaling (`"none"`) is to be applied. This should usually be `"sqrt"`.
`mass.weight`	Logical, indicating whether heavier masses receive higher weight. Should usually be TRUE.
`...`	Further arguments for the pseudospectrum plot (if shown).
`spec1, spec2`	Preprocessed pseudospectra, here two-column matrices where the first column is the (integer) m/z value, and the second column the (scaled) intensity.

Value

A vector of match factors.

Author(s)

Ron Wehrens

Examples

data(threeStdsNIST) ## gives smallDB, containing 78 patterns
data(threeStdsDB)   ## gives DB, containing 3 patterns :-D

matchExpSpec(DB[[1]]$pspectrum, smallDB, DB.treated = FALSE, plotIt = 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(metaMS)
Loading required package: CAMERA
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")'.

Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics

Attaching package: 'xcms'

The following objects are masked from 'package:Biobase':

    phenoData, phenoData<-

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metaMS/matchExpSpec.Rd_%03d_medium.png", width=480, height=480)
> ### Name: matchExpSpec
> ### Title: Match a GC-MS pseudospectrum to a database with a weighted
> ###   crossproduct criterion.
> ### Aliases: matchExpSpec mzmatch
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(threeStdsNIST) ## gives smallDB, containing 78 patterns
> data(threeStdsDB)   ## gives DB, containing 3 patterns :-D
> 
> matchExpSpec(DB[[1]]$pspectrum, smallDB, DB.treated = FALSE, plotIt = TRUE)
 [1] 0.7479017 0.7520501 0.7556286 0.7572973 0.7318883 0.7540335 0.7235683
 [8] 0.7329185 0.7299794 0.7520501 0.7693039 0.7693681 0.7306607 0.7604543
[15] 0.6874407 0.7184559 0.8237727 0.7184494 0.7411891 0.7676634 0.7447096
[22] 0.8047093 0.7603650 0.7293826 0.7375959 0.7422257 0.7430259 0.6919117
[29] 0.7087891 0.7608714 0.2042978 0.1960182 0.1925170 0.1987520 0.1987520
[36] 0.2090562 0.1981320 0.1919232 0.2026698 0.1975192 0.2076499 0.1982361
[43] 0.1037724 0.4168337 0.1287353 0.1304359 0.2710795 0.2722042 0.2133677
[50] 0.2704524 0.2676561 0.2505473 0.2722794 0.3887643 0.2133677 0.2600005
[57] 0.2650702 0.2895182 0.2141842 0.2714201 0.2845430 0.2869714 0.2788107
[64] 0.2936943 0.3087303 0.2672355 0.2172255 0.2333841 0.2560847 0.2310417
[71] 0.2347062 0.1581602 0.2103750 0.1968281 0.2066437 0.2269134 0.2055122
[78] 0.0000000
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>