Provide the corresponding enzyme sequence for an enzyme name

Description

This function is a small convenience function that reads in a prepared file with restriction enzyme sequence names and sequences. giveEnzymeSequence then provides restriction enzyme sequences for the example enzymes listed in van de Werken et al's 4Cseqpipe data base.

Usage

giveEnzymeSequence(fileNameDatabase, enzymeName)

Arguments

Value

Character string with the restriction enzyme sequence

Note

For any custom-made enzyme list it is assumed that there are no duplicate enzyme names in the database.

Author(s)

Carolin Walter

References

van de Werken, H., Landan, G., Holwerda, S., et al. (2012): Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nature Methods, 9, 969-971.

Examples

  file <- system.file("extdata", "enzymeData.csv", package="Basic4Cseq")  
  giveEnzymeSequence(file, "NlaIII")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Basic4Cseq)
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: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

The following object is masked from 'package:IRanges':

    runmean

The following object is masked from 'package:S4Vectors':

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/giveEnzymeSequence.Rd_%03d_medium.png", width=480, height=480)
> ### Name: giveEnzymeSequence
> ### Title: Provide the corresponding enzyme sequence for an enzyme name
> ### Aliases: giveEnzymeSequence
> ###   giveEnzymeSequence,character,character-method
> ### Keywords: giveEnzymeSequence
> 
> ### ** Examples
> 
>   file <- system.file("extdata", "enzymeData.csv", package="Basic4Cseq")  
>   giveEnzymeSequence(file, "NlaIII")
[1] "CATG"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>