read_inc_matrix: Read incidence matrix of proteomic identifications

In laurafancello/CCs4prot: Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Read incidence matrix of proteomic identifications

Description

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

Usage

read_inc_matrix(incM_filename, colnames_filename, rownames_filename)

Arguments

incM_filename	the name of the tab-delimited file containing incidence matrix values; the input incidence matrix must contain along the columns protein identifiers and along the rows peptides; each cell must contain a 1 or 0 value indicating whether or not the peptide maps on the corresponding protein.
colnames_filename	name of the file containing incidence matrix column names, which are protein identifiers. The file must contain one identifier per line. Protein identifiers must be in Ensembl format (i.e., ENSPXXXXXXXXXXX for human).
rownames_filename	name of the file containing incidence matrix row names, which are peptide identifiers. The file must contain one identifier per line. Peptide identifiers can be in any format (i.e. numeric identifiers, amino acid sequences, ...)

Value

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.

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)

laurafancello/CCs4prot documentation built on July 1, 2022, 1:34 p.m.