calSAMScore: Calculate SAM score

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

View source: R/calSAMScore.R

Description

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

Usage

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

Arguments

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.

Details

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.

Value

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

Author(s)

Wei Liu <[email protected]>

References

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

See Also

caltScore

Examples

1
2
3
4
	# 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)

cuihaibo1/123 documentation built on May 12, 2017, 2:20 p.m.