buildStringNetwork {glmSparseNet} | R Documentation |
This can reduce the dimension of the original network, as there may not be a mapping between peptide and gene id
buildStringNetwork(string.tbl, use.names = "protein")
string.tbl |
matrix with colnames and rownames as ensembl peptide id (same order) |
use.names |
default is to use protein names ('protein'), other options are 'ensembl' for ensembl gene id or 'external' for external gene names |
a new matrix with gene ids instead of peptide ids. The size of matrix can be different as there may not be a mapping or a peptide mapping can have multiple genes.
stringDBhomoSapiens
all.interactions.700 <- stringDBhomoSapiens(score_threshold = 700) string.network <- buildStringNetwork(all.interactions.700, use.names = 'external') # number of edges sum(string.network != 0)