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 |

`diseaseSample` |
a integer vector comprising the indexes of the disease (second class) samples in |

`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 <[email protected]>

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

1 2 3 4 |

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