DysGPS: DysGPS: Calculates Dysregulated gene pair score (DysGPS) for...

In DysPIA: Dysregulated Pathway Identification Analysis

Description

Calculates Dysregulated gene pair score (DysGPS) for each gene pair. Two-sample Welch's T test of gene pairs between case and control samples. The package 'DysPIAData' including the background data is needed to be loaded.

Usage

DysGPS(
  dataset,
  class.labels,
  controlcharacter,
  casecharacter,
  background = combined_background
)

Arguments

dataset	Matrix of gene expression values (rownames are genes, columnnames are samples).
class.labels	Vector of category labels.
controlcharacter	Charactor of control group in the class labels.
casecharacter	Charactor of case group in the class labels.
background	Matrix of the gene pairs' background. The default is 'combined_background', which includes real pathway gene pairs and randomly producted gene pairs. The 'combined_background' was incluede in 'DysPIAData'.

Value

A vector of DysGPS for each gene pair.

Examples

data(gene_expression_p53, class.labels_p53,sample_background)
DysGPS_sample<-DysGPS(gene_expression_p53, class.labels_p53,
 "WT", "MUT", sample_background)

DysPIA documentation built on July 10, 2020, 9:06 a.m.