find_variable_genes: Title find_variable_genes

In IOBR/IOBR: Immune Oncology Biological Research

Title find_variable_genes

Description

This function identifies variable genes based on specified criteria in a given gene expression dataset.

Usage

find_variable_genes(
  eset,
  data_type = c("count", "normalized"),
  methods = c("low", "mad"),
  prop = 0.7,
  quantile = c(0.75, 0.5, 0.25),
  min.mad = 0.1,
  feas = NULL
)

Arguments

eset	The gene expression dataset as a matrix.
data_type	(character, optional): The type of data in the dataset. Default is "count". Possible values: "count", "normalized".
methods	(character vector, optional): The methods to be used for gene selection. Default is c("low", "mad"). Possible values: "low", "mad".
prop	(numeric, optional): The proportion of samples in which a gene should be expressed. Default is 0.7.
quantile	(numeric vector, optional): The quantiles used to calculate the minimum allowable median absolute deviation (mad) value. Default is c(0.75, 0.5, 0.25).
min.mad	(numeric, optional): The minimum allowable mad value. Default is 0.1.
feas	(character vector, optional): Additional features to include in the variable gene selection. Default is NULL.

Author(s)

Dongqiang Zeng

Examples

# loading expression data
data("eset_tme_stad", package = "IOBR")
# Determination of filtration criteria
eset <- find_variable_genes(eset = eset_tme_stad, data_type = "normalized", methods = "mad", quantile = 0.25)

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.