Description Usage Arguments Value Author(s) References

Calculate the false discovery rate (FDR) by permutation for the group differences as calculated by SAM.

1 | ```
fdrSAM(G, y, nperms, tt.sam, alternative = "two.sided")
``` |

`G` |
Matrix of gene expression, columns ordered in the same order at the cell-frequency matrix (n by g, n samples, g genes) |

`y` |
A numeric vector of group association of each sample. Either 1 or 2. |

`nperms` |
Number of permutations to run. User responsability to the number appropriately fitting the sample size. |

`tt.sam` |
Real group comparison t-test statistic value |

`alternative` |
Type of test. Choices are 'two.sided','greater' or 'less' |

A list

`fdr.sam` |
A vector false dicovery rates for SAM comparison at different thresholds. A set of 100 theresholds is determined automatically from the data. |

`ncall.sam` |
Number of genes called significant at the given cutoff threshold with a FDR matching that indicated in fdr.sam |

`ttstar.sam` |
A matrix listing the t statistic for each gene in each permutation. (p by g, p permutations, g genes) |

`sigGene.sam` |
A vector of length equal to the number of genes being considered. For each gene the estimated FDR is listed. |

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). "Cell type-specific gene expression differences in complex tissues." _Nature methods_, *7*(4), pp. 287-9. ISSN 1548-7105, <URL: http://dx.doi.org/10.1038/nmeth.1439>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/20208531>.

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