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Add site-specific sequence information.

add_site_seq.Rd

This function adds a new "site_sequence" column to the variable information table. It is the protein sequence around the glycosylation site. If the head and tail amino acids of the peptide sequence are insufficient, fill with "X".

This function requires the following columns in the variable information tibble:

  • "protein": The protein uniprot accession.

  • "protein_site": The site on the protein sequence.

Usage

add_site_seq(exp, fasta = NULL, n_aa = 7, taxid = 9606)

# S3 method for class 'glyexp_experiment'
add_site_seq(exp, fasta = NULL, n_aa = 7, taxid = 9606)

# Default S3 method
add_site_seq(exp, fasta = NULL, n_aa = 7, taxid = 9606)

Arguments

exp

A glyexp::experiment() object with "glycoproteomics" type.

fasta

Either a file path to a FASTA file, a named character vector with protein IDs as names and sequences as value, or NULL to fetch from UniProt.

n_aa

The number of amino acids to the left and right of the glycosylation site. For example, if n_aa = 5, the resulting sequence will contain 11 amino acids.

taxid

NCBI taxonomy ID for UniProt lookup. Default: 9606 (human).

Value

A glyexp::experiment() object with the new "site_sequence" column.