proteome.example: An object of 'Proteome-class' representing the subset of...

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 subset of Drosophila melanogaster proteome.

Description

The subset Proteome-class of fruit fly.

Usage

proteome.example

Format

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

*‘proteome': ’data.frame': 1406 obs. of 4 variables *‘type': ’character': "UniProt" *‘species': ’character': "Drosophila melanogaster"

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) <- 7227

proteome <- prepareProteome(UniProt.ws)

proteome@proteome <- proteome@proteome[sample(1:19902, 1406), ]

Source

http://www.uniprot.org/

Examples

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

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