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

    ## 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)

[Package glmSparseNet version 1.8.1 Index]