discretize: Set the discretized expression attribute Uses the...

In csbl-usp/fcoex: FCBF-based Co-Expression Networks for Single Cells

Description

Set the discretized expression attribute Uses the discretize_exprs function of the FCBF package

Usage

discretize(
  fc,
  number_of_bins = 4,
  method = "varying_width",
  min_max_cutoff = 0.25
)

## S4 method for signature 'fcoex'
discretize(
  fc,
  number_of_bins = 4,
  method = "varying_width",
  min_max_cutoff = 0.25
)

Arguments

fc	Object of class fcoex
number_of_bins	Number of equal-width bins for discretization. Note: it is a binary discretization, with the first bin becoming one class ('low') and the other bins, another class ('high'). Defaults to 4.
method	Method applied to all genes for discretization. Methods available: "varying_width" (Binarization modulated by the number_of_bins param), "mean" (Split in ON/OFF by each gene mean expression), "median" (Split in ON/OFF by each gene median expression), "min_max_%" (Similat to the "varying width", a binarization threshold in a % of the min-max range is set. (minmax% param)),
min_max_cutoff	<- Modulator for the "min_max_%" method. Defaults to 0.25.

Value

A data frame with the discretized features in the same order as previously

Examples

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)

csbl-usp/fcoex documentation built on Sept. 15, 2021, 7:42 a.m.