Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 | DysGPS(
dataset,
class.labels,
controlcharacter,
casecharacter,
background = combined_background
)
|
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'. |
A vector of DysGPS for each gene pair.
1 2 3 | data(gene_expression_p53, class.labels_p53,sample_background)
DysGPS_sample<-DysGPS(gene_expression_p53, class.labels_p53,
"WT", "MUT", sample_background)
|
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