caltScore: Calculate tScore.
In cuihaibo1/drwPSurv_1.0.tar: DRW-GM

Description Usage Arguments Details Value Author(s) References See Also Examples

Calculate the t statistic and p-value of each gene in mRNA_matrix using the t-test.

1	caltScore(mRNA_matrix, normSample, diseaseSample)

`mRNA_matrix`	a p x n matrix of expression measurements with p genes and n samples.
`normSample`	a integer vector comprising the indexes of the normal (first class) samples in `mRNA_matrix`.
`diseaseSample`	a integer vector comprising the indexes of the disease (second class) samples in `mRNA_matrix`.

The function calculates the t statistic and p-value of each gene in mRNA_matrix using t-test. The output of the function will be used for topological weights and pathway activity inference.

a p x 2 matrix is returned, which contains the t statistic and p-value of p genes in mRNA_matrix.

Wei Liu <freelw@gmail.com>

Liu et al. Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

calSAMScore

	# calculates the t statistic and p-value of each gene using t-test between normal samples and
	# PCA samples in GSE8511
	data(GProf8511)
	tScore <- caltScore(GProf8511$mRNA_matrix, GProf8511$normal, GProf8511$PCA)