TDARACNE: TDARACNE

Description Usage Arguments Examples

View source: R/TDARACNE.R

Description

Main function, see P. Zoppoli, S. Morganella, M. Ceccarelli. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 2010, 11:154.

Usage

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TDARACNE(eSet,N,delta=3,likehood=1.2,norm=2,logarithm=1,thresh=0,ksd=1,tolerance=0.15,plot=FALSE,dot=FALSE,name="youHaveForgottenIt",adj=FALSE)

Arguments

eSet

eSet is the ExpressionSet object

N

N is respectively the number of bins in percentile normalization or in rank normalization

delta

delta is the maximum time delay allowed to infer connections

likehood

likehood is the fold change used as threshold to state the initial change expression (IcE)

norm

if you want column percentile normalization put norm == 1; if you want Rank normalization put norm == 2;

logarithm

if z is log put logarithm == 0;

thresh

the Influence threshold. if you have a threshold and a SD put them here in this format: c(thresh,SD) if you don't have threshold put 0 in thresh;

ksd

ksd is the standard deviation multiplier;

tolerance

tolerance is the DPI tolerance; 0 means no tolerance 1 means no DPI 0.15 is the default ARACNE tolerance as it is for TDARACNE

plot

plot must be TRUE to obtain automatically the graph

dot

dot must be TRUE to obtain a .dot file

name

name must be written with quotation marks(like this:'examplename') and is the name of the .dot file produced;

adj

adj must be TRUE to obtain an adjacent matrix

Examples

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	## take paper data
	library(TDARACNE)
	data(dataIRMAon)
	data(threshIRMAon)
	## main function; in output gives to you and adj matrix and a .dot file
# eSet is the ExpressionSet object
# N is respectively the number of bins in percentile normalization or in rank normalization
# delta is the maximum time delay allowed to infer connections
# likehood is the fold change used as threshold to state the initial change expression (IcE) 
# if you want column percentile normalization put norm == 1;
# if you want Rank normalization put norm == 2;
# if z is log put logarithm == 0;
# if you don't have threshold put 0 in thresh;
# ksd is the standard deviation multiplier;
# tolerance is the DPI tolerance;
# plot must be TRUE to obtain automatically the graph
# dot must be TRUE to obtain a .dot file 
# name must be written with quotation marks(like this:'examplename') and is the name of the .dot file produced;
# adj must be TRUE to obtain an adjacent matrix

TDARACNE(dataIRMAon,11,"netIRMAon",delta=3,likehood=1.2,norm=2,logarithm=1,thresh=threshIRMAon,ksd=0,tolerance=0.15);

TDARACNE documentation built on May 31, 2017, 10:58 a.m.

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