calculateTrypticity: Calculates level of trypticity for a list of LiP Peptides.

In devonjkohler/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Description

Takes as as input LiP data and a fasta file. These can be the outputs of MSstatsLiP functions.

Usage

calculateTrypticity(LiP_data, fasta_file)

Arguments

LiP_data	name of variable containing LiP data. Must contain at least two columns named 'PeptideSequence' and 'ProteinName'. The values in these column must match with what is in the corresponding FASTA file.
fasta_file	name of variable containing FASTA data. If FASTA file has not been processed please run the tidyFasta() function on it before inputting into this function.

Value

a data.frame including protein, peptide, and trypticity metrics.

Examples

fasta <- tidyFasta(system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP"))
calculateTrypticity(MSstatsLiP_data$LiP, fasta)

devonjkohler/MSstatsLiP documentation built on Dec. 19, 2021, 11:01 p.m.