conos: scanKModularity – R documentation

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scanKModularity

Scan joint graph modularity for a range of k (or k.self) values Builds graph with different values of k (or k.self if scan.k.self=TRUE), evaluating modularity of the resulting multilevel clustering NOTE: will run evaluations in parallel using con$n.cores (temporarily setting con$n.cores to 1 in the process)

Description

Usage

scanKModularity(
  con,
  min = 3,
  max = 50,
  by = 1,
  scan.k.self = FALSE,
  omit.internal.edges = TRUE,
  verbose = TRUE,
  plot = TRUE,
  ...
)

Arguments

`con`	Conos object to test
`min`	numeric Minimal value of k to test (default=3)
`max`	numeric Value of k to test (default=50)
`by`	numeric Scan step (default=1)
`scan.k.self`	boolean Whether to test dependency on scan.k.self (default=FALSE)
`omit.internal.edges`	boolean Whether to omit internal edges of the graph (default=TRUE)
`verbose`	boolean Whether to provide verbose output (default=TRUE)
`plot`	boolean Whether to plot the output (default=TRUE)
`...`	other parameters will be passed to con$buildGraph()

Value

a data frame with $k $m columns giving k and the corresponding modularity

Examples

library(pagoda2)
panel.preprocessed <- lapply(conosPanel::panel, basicP2proc, n.cores=1, min.cells.per.gene=0, 
    n.odgenes=2e3, get.largevis=FALSE, make.geneknn=FALSE)
con <- Conos$new(panel.preprocessed, n.cores=1)
scanKModularity(con)

conos

Clustering on Network of Samples

v1.4.0

GPL-3

Authors

Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]

Initial release