calculate_sequence_coverage: Protein sequence coverage

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Protein sequence coverage

Description

Calculate sequence coverage for each identified protein.

Usage

calculate_sequence_coverage(data, protein_sequence, peptides)

Arguments

data	a data frame containing at least the protein sequence and the identified peptides as columns.
protein_sequence	a character column in the data data frame that contains protein sequences. Can be obtained by using the function fetch_uniprot()
peptides	a character column in the data data frame that contains the identified peptides.

Value

A new column in the data data frame containing the calculated sequence coverage for each identified protein

Examples

data <- data.frame(
  protein_sequence = c("abcdefghijklmnop", "abcdefghijklmnop"),
  pep_stripped_sequence = c("abc", "jklmn")
)

calculate_sequence_coverage(
  data,
  protein_sequence = protein_sequence,
  peptides = pep_stripped_sequence
)

protti documentation built on Jan. 22, 2023, 1:11 a.m.