reduce_inc_matrix {net4pg}

Reduce size of incidence matrix for downstream analyses

Description

Reduce the size of the incidence matrix describing peptide-to-protein mappings to ease downstream analyses. The original incidence matrix is reduced to only contain proteins with at least one shared peptide and all peptides mapping on such proteins. This means that only proteins ambiguously identified are retained, which is the most interesting ones when studying ambiguity of protein identifications.

Usage

reduce_inc_matrix(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 logical matrix containing a smaller incidence matrix (with column and row names respectively reporting protein and peptide identifiers) and 0 or 1 values indicating whether or not the peptide maps on the corresponding protein. Only proteins with at least one shared peptide and all peptides mapping on such protein are reported in such reduced incidence matrix.

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)
# Only retain proteins with at least one shared peptide and all peptides
# mapping on such proteins.
incM_reduced <- reduce_inc_matrix(incM)