seq.example: example object of dagPeptides

In alyst/dagLogo: dagLogo

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

alyst/dagLogo documentation built on May 12, 2019, 2:32 a.m.