seq.example {dagLogo} | R Documentation

## example object of dagPeptides

### 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

[Package dagLogo version 1.20.0 Index]