example object of dagPeptides

Description

example object of dagPeptides

Usage

data(seq.example)

Format

An object of dagPeptides. The format is: A list.

data

'data.frame': 732 obs. of 7 variables

peptides

'matrix': amnio acid in each position

upstreamOffset

an integer, upstream offset position

downstreamOffset

an integer, downstream offset position

type

"character", type of identifiers

The format of data is

IDs

a character vector, input identifiers

anchorAA

a character vector, anchor amino acid provided in inputs

anchorPos

a numeric vector, anchor position in the protein

peptide

a character vector, peptide sequences

anchor

a character vector, anchor amino acid in the protein

upstream

a character vector, upstream peptides

downstream

a character vector, downstream peptides

Details

used in the examples seq obtained by: mart <- useMart("ensembl", "dmelanogaster_gene_ensembl") dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo")) seq <- fetchSequence(as.character(dat$entrez_geneid), anchorPos=as.character(dat$NCBI_site), mart=mart, upstreamOffset=7, downstreamOffset=7)

Examples

data(seq.example)
head(seq.example@peptides)
seq.example@upstreamOffset
seq.example@downstreamOffset

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(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/seq.example.Rd_%03d_medium.png", width=480, height=480)
> ### Name: seq.example
> ### Title: example object of dagPeptides
> ### Aliases: seq.example
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(seq.example)
> head(seq.example@peptides)
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] "L"  "F"  "P"  "K"  "G"  "F"  "D"  "K"  "V"  "S"   "M"   "P"   "S"   "G"  
[2,] "Q"  "A"  "A"  "L"  "E"  "S"  "N"  "K"  "K"  "A"   "F"   "R"   "S"   "W"  
[3,] "V"  "G"  "S"  "D"  "Q"  "A"  "G"  "K"  "Y"  "I"   "Y"   "E"   "R"   "A"  
[4,] "E"  "N"  "M"  "G"  "E"  "L"  "A"  "K"  "N"  "I"   "T"   "K"   "E"   "Q"  
[5,] "V"  "E"  "R"  "A"  "Q"  "K"  "L"  "K"  "V"  "N"   "A"   "G"   "H"   "V"  
[6,] "I"  "I"  "L"  "G"  "D"  "A"  "N"  "K"  "E"  "N"   "T"   "L"   "N"   "Q"  
     [,15]
[1,] "V"  
[2,] "S"  
[3,] "G"  
[4,] "G"  
[5,] "P"  
[6,] "L"  
> seq.example@upstreamOffset
[1] 7
> seq.example@downstreamOffset
[1] 7
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>