calSAMScore: Calculate SAM score
In cuihaibo1/DRWPClass: DRW-GM

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

Calculate the d statistic and q-value of each gene using the samr package.

1	calSAMScore(mRNA_matrix, normSample, diseaseSample, fdr.output = 0.05)

`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`.
`fdr.output`	(Approximate) False Discovery Rate cutoff for output in significant genes table.

The function calculates the d statistic and q-value of each gene in mRNA_matrix using the samr package. 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 d statistic and q-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.

caltScore

	# calculates the d statistic and q-value of each gene using SAM between normal samples and
	# PCA samples in GSE8511
	data(GProf8511)
	SAMScore <- calSAMScore(GProf8511$mRNA_matrix, GProf8511$normal, GProf8511$PCA, fdr.output = 0.2)