ensemble_biclusters: Convert communities into ensemble biclusters

In tdrose/mosbi: Molecular Signature identification using Biclustering

Convert communities into ensemble biclusters

Description

After calculation of communities with the get_louvain_communities function, the result can be converted into a list of bicluster objects with this function. Only biclusters are returned which have a minimum dimension of 2x2.

Usage

ensemble_biclusters(
  coms,
  bics,
  mat,
  row_threshold = 0.1,
  col_threshold = 0.1,
  threshold_sorted = FALSE
)

Arguments

coms	A list of communities (bicluster_nets) as outputted by get_louvain_communities.
bics	The list biclusters that was used for calculation with bicluster_network.
mat	The numeric matrix, that was used for biclustering.
row_threshold	Minimum fraction of biclusters of a community in which a row needs to occur so that it will be part of the outputted ensemble bicluster.
col_threshold	Minimum fraction of biclusters of a community in which a column needs to occur so that it will be part of the outputted ensemble bicluster.
threshold_sorted	Return the rows and columns in sorted by decreasing fraction.

Value

A list of bicluster objects.

Examples

b <- list(bicluster(row=c(1,2,3,4), column=c(1,2,3,4)),
    bicluster(row=c(3,4,5,6), column=c(3,4,5,6)))
# m <- matrix(runif(100), nrow=10)
# tm = matrix(c(0,1,1,0), nrow=2)
# bn <- list(bicluster_net(adjacency_matrix=tm, threshold=.5))
# ensemble_biclusters(bn, b, m)

tdrose/mosbi documentation built on May 4, 2022, 3:22 p.m.