peptide_stats: Calculate percentage of shared vs specific peptides

In laurafancello/net4pg: Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Calculate percentage of shared vs specific peptides

Description

Read in input the incidence matrix of peptide-to-protein mappings generated from valid proteomic identifications

Usage

peptide_stats(incM)

Arguments

incM	a logical matrix containing the incidence matrix with its column and row names (respectively, protein and peptide identifiers) and 0 or 1 values indicating whether or not the peptide maps on the corresponding protein.

Value

a list of three elements: i. number of shared peptides; ii. number of specific peptides; iii. percentage of specific peptides

Author(s)

Laura Fancello

Examples

# Read the tab-delimited file containing he proteome incidence matrix
incM_filename <- system.file( "extdata"
                             , "incM_example"
                             , package = "net4pg"
                             , mustWork = TRUE)
rownames_filename <- system.file( "extdata"
                                  , "peptideIDs_incM_example"
                                  , package = "net4pg"
                                  , mustWork = TRUE)
colnames_filename <- system.file( "extdata"
                                 , "proteinIDs_incM_example"
                                 , package = "net4pg"
                                 , mustWork = TRUE)
incM <- read_inc_matrix(incM_filename = incM_filename
                 , colnames_filename = colnames_filename
                 , rownames_filename = rownames_filename)
# Calculate percentage of shared vs specific peptides
peptideStatsOut <- peptide_stats(incM = incM)

laurafancello/net4pg documentation built on July 1, 2022, 1:34 p.m.