bootcluster (version 0.4.2)

threshold.select: Estimate of the overall Jaccard stability

Description

Estimate of the overall Jaccard stability

Value

stabilityresult

a list of result for nodes-wise stability

modularityresult

a list of modularity information with each candidate threshold

jaccardresult

a list estimated unconditional observed stability and the estimates of expected stability under the nul

originalinformation

a list information for original data, igraph object and adjacency matrix constructed with each candidate threshold

threshold.seq

a list of candicate threshold given to the function

Arguments

data.input

a data.frame of the data set where the rows are observations and columns are covariates

threshold.seq

a numeric sequence of candidate threshold

B

number of bootstrap re-samplings

cor.method

the correlation method applied to the data set,three method are available: "pearson", "kendall", "spearman".

large.size

the smallest set of modules, the large.size=0 is recommended to use right now.

PermuNo

number of random graphs for the estimation of expected stability

no_cores

a interger number of CPU cores on the current host (This function can't not be used yet).

Author

Mingmei Tian

Details

threshold.select is used to estimate of the overall Jaccard stability from a sequence of given threshold candidates, threshold.seq.

References

A framework for stability-based module detection in correlation graphs. Mingmei Tian,Rachael Hageman Blair,Lina Mu, Matthew Bonner, Richard Browne and Han Yu.

Examples

# \donttest{
set.seed(1)
data(wine)
x0 <- wine[1:50,]

mytest<-threshold.select(data.input=x0,threshold.seq=seq(0.5,0.8,by=0.05), B=20, 
cor.method='pearson',large.size=0,
PermuNo = 10,
no_cores=1,
scheme_2 = FALSE)
# }