R: Function computing heuristically the required number of...
calculateNrPeaks
R Documentation
Function computing heuristically the required number of consecutive aggregated isotopic variants.
Description
Function computing heuristically the required number of consecutive aggregated isotopic variants (starting from the monoisotopic mass).
Usage
calculateNrPeaks(aC)
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).
Details
This function uses following rule of thumb: the difference between the theoretical monoisotopic mass and the theoretical average mass is
computed and multiplied by two. Subsequently, the obtained number is rounded to the nearest integer greater than or equal to
the multiplied difference. For small molecules, the minimal number of returned variants is five.
Value
Integer number not lower than 5.
Author(s)
Jurgen Claesen <jurgen.claesen@uhasselt.be>
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
See Also
useBRAIN
Examples
aC <- list(C=23832, H=37816, N=6528, O=7031, S=170) # Human dynein heavy chain
res <- calculateNrPeaks(aC = aC)
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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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/calculateNrPeaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateNrPeaks
> ### Title: Function computing heuristically the required number of
> ### consecutive aggregated isotopic variants.
> ### Aliases: calculateNrPeaks
>
> ### ** Examples
>
> aC <- list(C=23832, H=37816, N=6528, O=7031, S=170) # Human dynein heavy chain
> res <- calculateNrPeaks(aC = aC)
>
>
>
>
>
> dev.off()
null device
1
>