ecoli.proteome: An object of 'Proteome-class' representing the _Escherichia...

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

An object of Proteome-class representing the Escherichia coli proteome.

Description

A dataset containing the E. coli proteome.

Usage

ecoli.proteome

Format

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

*‘proteome': ’data.frame': 13780 obs. of 4 variables *‘type': ’character': "UniProt" *‘species': ’character': "Escherichia coli"

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 as an example dataset

Annotation data obtained by:

library(UniProt.ws)

taxId(UniProt.ws) <- 562

proteome <- prepareProteome(UniProt.ws, species="Escherichia coli")

Source

http://www.uniprot.org/

Examples

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

jianhong/dagLogo documentation built on Nov. 5, 2024, 7:46 a.m.