cc_composition: Get peptides and peptide-to-protein mappings for each...

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

Get peptides and peptide-to-protein mappings for each connected component

Description

Get peptides and peptide-to-protein mappings for each connected component. For each connected component, first extract its protein members; then, extract all specific and shared peptides mapping on those protein; finally, extract the subset of incidence matrix representing peptide-to-protein mappings.

Usage

cc_composition(cc.proteins, incM)

Arguments

cc.proteins	a list of vectors (one for each connected component), each enumerating the proteins members of a connected component.
incM	a logical matrix containing the incidence matrix with its column and row names (respectively, protein and peptide identifiers) names and 0 or 1 values indicating whether or not the peptide maps on the corresponding protein.

Value

a list of two elements: i. a list of vectors (one for each connected component) enumerating peptides mapping on protein members of each connected component; ii. a list of matrices or vectors (one for each connected component) representing peptide-to-protein mappings for each connected component; matrices are used if multiple peptides identify protein members of that connected component, vectors if only a single peptide.

Author(s)

Laura Fancello

Examples

# Read the tab-delimited file containing the 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)
# Only retain proteins with at least one shared peptide and all peptides
# mapping on such proteins.
incM_reduced <- reduce_inc_matrix(incM)
# Generate adjacency matrix describing protein-to-protein mappings
adjM <- get_adj_matrix(incM_reduced)
# Generate graph of protein-to-protein connections and calculate its
# connected component
multProteinCC <- get_cc(adjM)
# For each connected component, extract peptides mapping on its protein
# members and the subset of the incidence matrix describing peptide-to-protein
# mapping
cc.peptides.incM <- cc_composition(cc.proteins = multProteinCC$cc
                                  , incM = incM)

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