pep_encode_mat: Encode a peptide

Description Usage Arguments Details Value Examples

View source: R/utils_pep.R

Description

Peptides are encoded using the BLOSUM62 probability matrix (See BLOSUM62_PROB data matrix)

Usage

1

Arguments

pep

A character vector of peptides to be encoded

Details

Each position in the peptide become a vector of 20 values, corresponding to the rounded log odds ratio for substituting the amino acid in the peptide with each of the 20 standard proteogenic amino acids.

The final result is a tibble with as many rows as input peptides and number columns equal to the number of positions in the input peptides times the number of BLOSUM62 substitions values (20) plus a column with the input peptides. For 100 9-mers this yields 100 rows and 181 columns

Value

A tibble of encoded peptides

Examples

1
2
pep_encode_mat(pep_ran(k=9,n=100))
dim(pep_encode_mat(pep_ran(k=9,n=100)))

leonjessen/PepTools documentation built on Feb. 23, 2018, 6:36 p.m.