buildStringNetwork {glmSparseNet}R Documentation

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(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


  all.interactions.700 <- stringDBhomoSapiens(score_threshold = 700)
  string.network       <- buildStringNetwork(all.interactions.700,
                                              use.names = 'external')
  # number of edges
  sum(string.network != 0)


[Package glmSparseNet version 1.12.0 Index]