quantile_test: Simple test of gene expression variations in a serie of...

In CDecamps/penda: A R package that performs personalized differential analysis of comics data

Simple test of gene expression variations in a serie of samples

Description

This function makes the quantile test of the dysregulation of all genes. The patient's gene is compared at the gene expression in controls sample.

Usage

quantile_test(controls, samples, quant, factor)

Arguments

controls	A matrix with genes expressions in controls for all the patients.
samples	A vector or a matrix with all the genes expressions for each sample.
quant	The quantile of the control genes expression, quantile(c(quant, 1-quant)).
factor	The factor for the quantile. The down-regulated limit will be quantmin/factor, and the up-regulated limit quantmax*factor.

Value

This function return a list with two vectors or matrix : D, with TRUE for genes down-regulated U, with TRUE for genes up-regulated.

Examples

# First, load and define the data
controls = penda::penda_data_ctrl[1:10, 1:10]
samples = penda::penda_data_case[1:10, 1:3]
# Second, test is the expression is deregulated for each gene of a sample
res_quantile = penda::quantile_test(controls,
                                samples,
                                quant = 0.03,
                                factor = 1.4)

CDecamps/penda documentation built on March 29, 2024, 3:26 a.m.