seq.example: An object of 'dagPeptides-class' representing acetylated...

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

An object of dagPeptides-class representing acetylated lysine-containing peptides.

Description

A dataset containing the acetylated lysine-containing peptides from Drosophila melanogaster.

Usage

seq.example

Format

An object of dagPeptides-class Class 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 as an example dataset

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

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