single.network.module {sidier}

Get modules and network given a threshold

Description

Gets details on modules and connections in the network connecting nodes showing distances equal or lower than the defined threshold value.

Usage

single.network.module(dis,threshold=NA,refer2max=TRUE,out="module",
save.file=FALSE,modFileName="Modules_summary.txt")

Arguments

dis

the distance matrix to be represented

threshold

a numeric between 0 and 1, is the value of the maximum distance to be considered as a link. This value is referred to the maximum distance in the input matrix (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 32% of the maximum distance found in the distance matrix).

refer2max

a logic, "TRUE" to refer the threshold value to the maximum distance in the input matrix (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 32% of the maximum distance found in the distance matrix). "FALSE" to refer the threshold to a specific value (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 0.32, regardless the maximum distance found in the distance matrix).

out

a string, the type of output, "module" to get a matrix with two columns giving each sequence name and the module it belongs to, and "network" to get a square matrix representing connection (1) or lack of connection (0) between sequences in the network.

save.file

a logic, "TRUE" to save the summary of network modules, attributing every individual to a module.

modFileName

(if modules=TRUE) the name of a generated file containing a summary of module results

Author(s)

A. J. Muñoz-Pajares

See Also

perc.thr, NINA.thr

Examples

#generating distance matrix:
dis<-matrix(nrow=12,c(0.0000,0.5000,0.1875,0.5000,0.6250,0.5000,0.2500,0.6250,
0.3750,0.3750,0.3750,0.3750,0.5000,0.0000,0.7500,0.0000,0.6250,0.0000,0.8750,
0.6250,0.3750,0.3750,0.3750,0.3750,0.1875,0.7500,0.0000,0.7500,0.8750,0.7500,
0.2500,0.8750,0.6250,0.6250,0.6250,0.6250,0.5000,0.0000,0.7500,0.0000,0.6250,
0.0000,0.8750,0.6250,0.3750,0.3750,0.3750,0.3750,0.6250,0.6250,0.8750,0.6250,
0.0000,0.6250,0.5000,0.0000,0.2500,0.2500,0.2500,0.2500,0.5000,0.0000,0.7500,
0.0000,0.6250,0.0000,0.8750,0.6250,0.3750,0.3750,0.3750,0.3750,0.2500,0.8750,
0.2500,0.8750,0.5000,0.8750,0.0000,0.5000,0.5000,0.5000,0.5000,0.5000,0.6250,
0.6250,0.8750,0.6250,0.0000,0.6250,0.5000,0.0000,0.2500,0.2500,0.2500,0.2500,
0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,0.0000,0.0000,
0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,0.0000,
0.0000,0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,
0.0000,0.0000,0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,
0.0000,0.0000,0.0000,0.0000))
row.names(dis)<-c("Population1_sequence1","Population1_sequence2",
"Population1_sequence3","Population1_sequence4","Population2_sequence1",
"Population2_sequence2","Population2_sequence3","Population2_sequence4",
"Population3_sequence1","Population3_sequence2","Population3_sequence3",
"Population3_sequence4")
colnames(dis)<-row.names(dis)

# #Representing distances equal or lower than 37% of the maximum distance:
# single.network.module(dis=dis,threshold=0.37)
# single.network.module(dis=dis,threshold=0.37,out="network")
# 
# # Compare these outputs with:
# single.network(dis=dis,threshold=0.37,label=paste(substr(row.names(dis),11,11),
# substr(row.names(dis),21,21),sep="-"))