prepare an object of dagPeptides from sequences

Description

prepare an object of dagPeptides from sequences

Usage

formatSequence(seq, proteome, upstreamOffset, downstreamOffset)

Arguments

Value

return an object of dagPeptides, which is a list contains: data, peptides, upstreamOffset, downstreamOffset and type information

Author(s)

Jianhong Ou, Julie Zhu

See Also

fetchSequence

Examples

if(interactive()){
    dat <- unlist(read.delim(system.file("extdata", 
                            "grB.txt", package="dagLogo"), 
                            header=F, as.is=TRUE))
    proteome <- prepareProteome(fasta=system.file("extdata", 
                                              "HUMAN.fasta",
                                              package="dagLogo"))
    seq <- formatSequence(dat, proteome)
}

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 'license()' or 'licence()' for distribution details.

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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.
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> library(dagLogo)
Loading required package: biomaRt
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: motifStack
Loading required package: MotIV
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


Attaching package: 'MotIV'

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

    filter

Loading required package: ade4

Attaching package: 'ade4'

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

    score

Loading required package: Biostrings
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dagLogo/formatSequence.Rd_%03d_medium.png", width=480, height=480)
> ### Name: formatSequence
> ### Title: prepare an object of dagPeptides from sequences
> ### Aliases: formatSequence
> ### Keywords: misc
> 
> ### ** Examples
> 
> #if(interactive()){
>     dat <- unlist(read.delim(system.file("extdata", 
+                             "grB.txt", package="dagLogo"), 
+                             header=F, as.is=TRUE))
>     proteome <- prepareProteome(fasta=system.file("extdata", 
+                                               "HUMAN.fasta",
+                                               package="dagLogo"))
>     seq <- formatSequence(dat, proteome)
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>