Implementation of BRAIN (Baffling Recursive Algorithm for Isotope distributioN calculations)

Description

This package implements BRAIN (Baffling Recursive Algorithm for Isotope distributioN calculations) is described in full details by Claesen et al. The algorithm uses an algebraic approach (Viete's formulas, Newton identities [Macd]) which is especially useful for large molecules due to its advantageous scaling properties. This version of the package provides functions for calculating the aggregated isotopic distribution and center-masses masses for each aggregated isotopic variant for chemical components built from carbon, hydrogen, oxygen, nitrogen and sulfur (e.g. peptides). The natural abundances and molecular masses for stable isotopes of C, H, N, O, S are taken from IUPAC 1997 [Rosm].

Details

Author(s)

Piotr Dittwald with contribution of Dirk Valkenborg and Jurgen Claesen

Maintainer: Piotr Dittwald <piotr.dittwald@mimuw.edu.pl>

References

[Clae] Claesen J., Dittwald P., Burzykowski T. and Valkenborg D. An efficient method to calculate the aggregated isotopic distribution and exact center-masses. JASMS, 2012, doi:10.1007/s13361-011-0326-2

[Macd] Macdonald I.G., Symmetric functions and Hall polynomials / by I. G. Macdonald. Clarendon Press; Oxford University Press, Oxford : New York, 1979.

[Rosm] K.J.R. Rosman and P.D.P. Taylor. Isotopic compositions of the elements 1997. Pure and Applied Chemistry, 70(1):217-235, 1998.

Examples

  nrPeaks = 1000
  aC <-  list(C=23832, H=37816, N=6528, O=7031, S=170)  # Human dynein heavy chain  
  res <- useBRAIN(aC = aC, nrPeaks = nrPeaks)
  iso <- res$isoDistr
  masses <- res$masses
  mono <- res$monoisotopicMass
  avgMass <- res$avgMass

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.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(BRAIN)
Loading required package: PolynomF
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BRAIN/BRAIN-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BRAIN-package
> ### Title: Implementation of BRAIN (Baffling Recursive Algorithm for
> ###   Isotope distributioN calculations)
> ### Aliases: BRAIN-package BRAIN
> ### Keywords: package
> 
> ### ** Examples
> 
>   nrPeaks = 1000
>   aC <-  list(C=23832, H=37816, N=6528, O=7031, S=170)  # Human dynein heavy chain  
>   res <- useBRAIN(aC = aC, nrPeaks = nrPeaks)
>   iso <- res$isoDistr
>   masses <- res$masses
>   mono <- res$monoisotopicMass
>   avgMass <- res$avgMass
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>