nmf.gene.choose.k: A Function to find responsible genes for variation within a...

In ASharmaML/nmf-gene:

Description

This function allows you to find the likely genes responsible for affecting a variable, typically the presence or absence of a disease

Usage

nmf.gene.choose.k(k.range = seq(2, ncol(gene_expressions)/10, 2),
  gene_expressions, zero.threshold = 0.1, log.scaled = T,
  loss.type = "mse", b = c(0, 0, 0), na = FALSE, sample = FALSE,
  number.genes, a = c(0, 0, 0))

Arguments

k.range	Suggest a vector of k values to explore, with a default
zero.threshold	what proportion of zeros should a gene have before being left out of the analysis
number.genes	The number of likely genes to find
variable	The discrete variable or disease to be investigated
gene.names	A character/string vector containing the list of gene names
gene.expressions	The initial gene expression matrix, with genes labelled by row names

Examples

nmf.responsible.genes()

ASharmaML/nmf-gene documentation built on May 14, 2019, 8:57 a.m.