find_cbf_modules: find_cbf_modules
In lubianat/fcoex: FCBF-based Co-Expression Networks for Single Cells

Description Usage Arguments Details Value Examples

find_cbf_modules uses Symmetrical Uncertainty as a correlation measure and the FCBF algorithm to

find_cbf_modules(fc, n_genes = NULL, FCBF_threshold = 0.1,
  verbose = TRUE, is_parallel = FALSE)

## S4 method for signature 'fcoex'
find_cbf_modules(fc, n_genes = NULL,
  FCBF_threshold = 0.1, verbose = TRUE, is_parallel = FALSE)

`fc`	A fcoex object containing a discretized expression table
`n_genes`	Sets the number of genes to be selected in the first part of the algorithm. If left unchanged, it defaults to NULL and the thresh parameter is used. Caution: it overrides the thresh parameter altogether.
`FCBF_threshold`	A threshold for the minimum correlation (as determined by symettrical uncertainty) between each variable and the class used for wrapped FCBF function. Defaults to 0.1.
`verbose`	Adds verbosity. Defaults to TRUE
`is_parallel`	Uses package parallel to paralleliza calculations. Defaults to FALSE.

1 - Filter the gene list by correlations to a class (Step 1)

and

2 - Determine soft thresholds for coexpression to genes predominantly correlated to a class.

Returns a list with the CBF modules found or a adjacency matrix of the graph

library(SingleCellExperiment) 
data("mini_pbmc3k")
targets <- colData(mini_pbmc3k)$clusters
exprs <- as.data.frame(assay(mini_pbmc3k, "logcounts"))
fc <- new_fcoex(exprs, targets)
fc <- discretize(fc)
fc <- find_cbf_modules(fc)