seq.example {dagLogo} | R Documentation |
example object of dagPeptides
data(seq.example)
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
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)
data(seq.example) head(seq.example@peptides) seq.example@upstreamOffset seq.example@downstreamOffset