buildStringNetwork: Build gene network from peptide ids

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

Description

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

Usage

buildStringNetwork(string.tbl, use.names = "protein")

Arguments

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

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

## Not run: 
  all.interactions.700 <- stringDBhomoSapiens(score_threshold = 700)
  string.network       <- buildStringNetwork(all.interactions.700,
                                              use.names = 'external')
  # number of edges
  sum(network != 0)

## End(Not run)

glmSparseNet documentation built on April 14, 2021, 6 p.m.