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Last data update: 2014.03.03

R: Function computing probabilities of aggregated isotopic...

useBRAIN

R Documentation

Function computing probabilities of aggregated isotopic variants and their center-masses using BRAIN algorithm.

Description

Function computing probabilities of isotopic variants and their aggregated masses for chemical components composed of carbon, hydrogen, oxygen, nitrogen and sulfur (e.g. peptides). Additionally the function returns also the monoisotopic mass and the average mass of given chemical component.

Usage

useBRAIN(aC, stopOption = "nrPeaks", nrPeaks, coverage, abundantEstim)

Arguments

`aC`	List with fields C, H, N, O, S of integer non-negative values (if any field is ommited, then its value is set to 0).
`stopOption`	one of the following strings: "nrPeaks" (default), "coverage", "abundantEstim"
`nrPeaks`	Integer indicating the number of consecutive isotopic variants to be calculated, starting from the monoisotopic one. This value can always be provided, even if <stop.option> is not a default setting. In the latter case it is a hard stopping criterion.
`coverage`	Scalar indicating the value of the cumulative aggregated distribution. The calculations will be stopped after reaching this value.
`abundantEstim`	Integer indicating the number of consecutive isotopic variants to be calculated, starting from one after the most abundant one. All consecutive isotopic variants before the most abundant peak are also returned.

Details

Function uses recursive formulae based on algebraic Newton-Girard identity (see [Clae]).

Value

Named list with the following fields:

isoDistrProbabilities of aggregated isotopic variants (numeric vector)
massesAggregated masses for isotopic variants (numeric vector)
monoisotopicMassMonoisotopic mass (numeric)
avgMassAverage mass - weighted average of the isotopic variants contributing to the most abundant aggregated variant (numeric)

Note

Remember that the isotopic variants starts from monoisotopic one. For large chemical molecules, first masses may have very low abundances. So sufficient number of peaks should be calculated to reach most abundant isotopic variant.

If only isotopic probabilities are needed, then the function calculateIsotopicProbabilities should be used.

Author(s)

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

Examples

  nrPeaks = 1000  
  aC <-  list(C=23832, H=37816, N=6528, O=7031, S=170)  # Human dynein heavy chain  
  res <-  useBRAIN(aC = aC, stopOption="nrPeaks", nrPeaks = nrPeaks)

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(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/useBRAIN.Rd_%03d_medium.png", width=480, height=480)
> ### Name: useBRAIN
> ### Title: Function computing probabilities of aggregated isotopic variants
> ###   and their center-masses using BRAIN algorithm.
> ### Aliases: useBRAIN
> 
> ### ** Examples
> 
>   nrPeaks = 1000  
>   aC <-  list(C=23832, H=37816, N=6528, O=7031, S=170)  # Human dynein heavy chain  
>   res <-  useBRAIN(aC = aC, stopOption="nrPeaks", nrPeaks = nrPeaks)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>