DysGPS {DysPIA}

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

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)