the subset proteome of Escherichia coli

Description

the subset proteome of Escherichia coli

Usage

data(ecoli.proteome)

Format

An object of Proteome for Escherichia coli proteome. The format is: A list with one data frame and an character.

proteome

'data.frame': obs. of 4 variables

type

'character': "UniProt"

The format of proteome is

ENTREZ_GENE

a character vector, records entrez gene id

SEQUENCE

a character vector, peptide sequences

ID

a character vector, Uniprot ID

LEN

a character vector, length of peptides

Details

used in the examples Annotation data obtained by: library(UniProt.ws) taxId(UniProt.ws) <- 562 proteome <- prepareProteome(UniProt.ws, species="Escherichia coli")

Examples

data(ecoli.proteome)
head(ecoli.proteome@proteome)
ecoli.proteome@type

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/ecoli.proteome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ecoli.proteome
> ### Title: the subset proteome of Escherichia coli
> ### Aliases: ecoli.proteome
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ecoli.proteome)
> head(ecoli.proteome@proteome)
  ENTREZ_GENE
1    13877411
2    13877411
3    10076131
4    10076131
5    10076142
6    10076142
                                                                                                                                                                                                                                                                                        SEQUENCE
1                      MKLKQNIEKEIIKINNIRIHQYTVLYTSNCTIDVYTKEGSNTYLRNELIFLERGINISVRLQKKKSTVNPFIAIRLSSDTLRRLKDALMIIYGISKVDACSCPNWSKGIIVADADDSVLDTFKSIDHNDDSRITSDLIYLISKIENNRKIIESIYISAVSFFSDKVRNTIEKDLSKRWTLAIIADEFNVSEITIRKRLESEYITFNQILMQSRMSKAALLLLDNSYQISQISNMIGFSSTSYFIRLFVKHFGITPKQFLTYFKSQ
2                      MKLKQNIEKEIIKINNIRIHQYTVLYTSNCTIDVYTKEGSNTYLRNELIFLERGINISVRLQKKKSTVNPFIAIRLSSDTLRRLKDALMIIYGISKVDACSCPNWSKGIIVADADDSVLDTFKSIDHNDDSRITSDLIYLISKIENNRKIIESIYISAVSFFSDKVRNTIEKDLSKRWTLAIIADEFNVSEITIRKRLESEYITFNQILMQSRMSKAALLLLDNSYQISQISNMIGFSSTSYFIRLFVKHFGITPKQFLTYFKSQ
3 MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
4 MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
5 MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
6 MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
      ID LEN
1 P43464 265
2 Q7BBX3 265
3 P62593 286
4 Q6SJ61 286
5 P62593 286
6 Q6SJ61 286
> ecoli.proteome@type
[1] "UniProt"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>