tacs: Calculate Control Strength toward every nodes on directed...

In takenakayoichi/tacs: Time Course Analysis of Control strength toward nodes/gene expression on directed graph based on Information Criterion.

Description

Calculate Control Strength toward every nodes on directed graph based on information criterion

Calculate Control Strength toward every nodes on directed graph based on information criterion

Usage

tacs(network, exp_data, ic_type = "aic-g", is_markov = FALSE,
  segment = NA, segment_name = NA)

Arguments

network	directed graph: format used in library bnlearn is used.
exp_data	experimental data on nodes in the network: data frame
ic_type	information criterion type: string "aic"(=default) or "bayes"
is_markov	edges are drown under markov property :boolean TRUE or FALSE(=default)
segment	This paramer assigns the segments of exp_data. It is used when exp_data is composed of plural time-course experiment and the edges are drown under markov property
segment_name	name list of segments. default (seg1,seg2,...)

Value

strength Control strength toward each node for every time point: data frame

Examples

data(diauxie)#an example in GIW2015 paper
res <- tacs(diauxie$net,diauxie$exp,"aic-g",is_markov=TRUE,segment=diauxie$segment,segment_name=diauxie$segment_name)
gene_selected <- apply(res$score,2,max) + res$ave_InfoGain >0
score <- res$score[1:16,gene_selected] # 1:16: Wild Type.
score[score<0] <- 0  #to show the results in barplot, remove negatives
barplot(t(as.matrix(score)),width=nrow(score),beside=TRUE,
col=topo.colors(ncol(score)),legend.text=names(score))
WT <-  select.segments(res,"WT") #Plot score of each gene
WT_genes <- select.nodes(WT,names(gene_selected[gene_selected]))
plot(WT_genes)
data(dream4) #Anther example
tacs(dream4$net,dream4$exp,"aic-g",TRUE,dream4$segment,NA) -> res

takenakayoichi/tacs documentation built on May 31, 2019, 2:50 a.m.