tna.graph {RTN} | R Documentation

## Compute a graph from TNA objects (deprecated function).

### Description

This function is provided for compatibility with older versions of ‘RTN’ only, and will be defunct at the next release (see details).

### Usage

    tna.graph(object, tnet = "dpi", gtype="rmap", minRegulonSize=15, tfs=NULL,
    amapFilter="quantile", amapCutoff=NULL, ...)

### Arguments

`object` | an object of class 'TNA' `TNA-class`.
`tnet` | a single character value specifying which network information should be used to compute the graph. Options: "ref" and "dpi".
`gtype` | a single character value specifying the graph type. Options: "rmap" and "amap". The "rmap" option returns regulatory maps represented by TFs and targets (regulons) and "amap" computes association maps among regulons (estimates the overlap using the Jaccard Coefficient).
`minRegulonSize` | a single integer or numeric value specifying the minimum number of elements in a regulon. Regulons with fewer than this number are removed from the graph.
`tfs` | a vector with transcription factor identifiers.
`amapFilter` | a single character value specifying which method should be used to filter association maps (only when gtype="amap"). Options: "phyper","quantile" and "custom".
`amapCutoff` | a single numeric value (>=0 and <=1) specifying the cutoff for the association map filter. When amapFilter="phyper", amapCutoff corresponds to a pvalue cutoff; when amapFilter="quantile", amapCutoff corresponds to a quantile threshold; and when amapFilter="custom", amapCutoff is a JC threshold.
`...` | additional arguments passed to tna.graph function.

### Details

The following function is deprecated and will be made defunct; use the replacement indicated below:

- tna.graph: `tni.graph`

### Value

a graph object.

### Author(s)

Mauro Castro

[Package RTN version 2.10.1 Index]