discretize_exprs: discretize_exprs Simple discretizing of gene expression

In FCBF: Fast Correlation Based Filter for Feature Selection

Description

This function takes the range of values for each gene in a previously normalized expression table (genes/variables in rows, samples/ observations in columns) and uses it for a width-based discretization. Each feature is divide into "n" bins of equal width. The first bin is attributed the class 'low' and the next bins are assigned to "high". It transposes the original expression table.

Usage

discretize_exprs(
  expression_table,
  number_of_bins = 3,
  method = "varying_width",
  alpha = 1,
  centers = 3,
  min_max_cutoff = 0.25,
  progress_bar = TRUE
)

Arguments

expression_table	A previously normalized expression table Note: this might drastically change the number of selected features.
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 3.
method	Method applied to all genes for discretization. Methods available: "varying_width" (Varying width binarization, default, described in function description. 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), "mean_sd"(Split in low/medium/high by each assigning "medium" to the interval between mean +- standard_deviation. Modulated by the alpha param, which enlarges (>1) or shrinks (<1) the "medium" interval. ), ), "kmeans"(Split in different groups by the kmeans algorithm. As many groups as specified by the centers param) and "min_max_percent" (Similat to the "varying width", a binarization threshold in a percent of the min-max range is set. (minmaxpercent param)), "GMM" (A Gaussian Mixture Model as implemented by the package mclust, trying to fit 2:5 Gaussians)
alpha	Modulator for the "mean_sd" method.Enlarges (>1) or shrinks (<1) the "medium" interval. Defaults to 1.
centers	Modulator for the "kmeans" method. Defaults to 3.
min_max_cutoff	<- Modulator for the "min_max_percent" method. Defaults to 0.25.
progress_bar	Enables a progress bar for the discretization. Defaults to TRUE.

Value

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

Examples

data(scDengue)
exprs <- SummarizedExperiment::assay(scDengue, 'logcounts')
discrete_expression <- as.data.frame(discretize_exprs(exprs))
head(discrete_expression[, 1:4])

FCBF documentation built on Nov. 8, 2020, 8:30 p.m.