make_labels {PrInCE} | R Documentation |
Create labels for a classifier for protein pairs in the same order as in a dataset that will be used as input to a classifier, in a memory-friendly way.
make_labels(gold_standard, dat, node_columns = c(1, 2), protein_groups = NULL)
gold_standard |
an adjacency matrix of gold-standard interactions |
dat |
a data frame with interacting proteins in the first two columns |
node_columns |
a vector of length two, denoting either the indices
(integer vector) or column names (character vector) of the columns within
the data frame containing the nodes participating in pairwise interactions;
defaults to the first two columns of the data frame ( |
protein_groups |
optionally, specify a list linking each protein in the first two columns of the input data frame to a protein group |
a vector of the same length as the input dataset, containing
NA
s for protein pairs not in the gold standard and ones or zeroes
based on the content of the adjacency matrix
data(gold_standard) adj <- adjacency_matrix_from_list(gold_standard) proteins <- unique(unlist(gold_standard)) dat <- data.frame(protein_A = sample(proteins, 10), protein_B = sample(proteins, 10)) labels <- make_labels(adj, dat)