buildStringNetwork: Build gene network from peptide ids

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

Build gene network from peptide ids

Description

This can reduce the dimension of the original network, as there may not be a mapping between peptide and gene id

Usage

buildStringNetwork(
  stringTbl,
  useNames = c("protein", "ensembl", "external"),
  string.tbl = deprecated(),
  use.names = deprecated()
)

Arguments

stringTbl	data.frame or tibble with colnames and rownames as ensembl peptide id (same order).
useNames	character(1) that defaults to use protein names _('protein'), other options are 'ensembl' for ensembl gene id or 'external' for external gene names.
string.tbl
use.names

Value

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.

See Also

stringDBhomoSapiens()

Examples

interactions <- stringDBhomoSapiens(scoreThreshold = 100)
string_network <- buildStringNetwork(interactions)

# number of edges
sum(string_network != 0)

sysbiomed/glmSparseNet documentation built on Feb. 17, 2024, 1:38 p.m.