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:

Value

a graph object.

Author(s)

Mauro Castro


[Package RTN version 2.10.1 Index]