Description Usage Arguments Value Author(s) References

Computes the constrast between groups for the deconvolved cell-specific expression for each cell-type

1 2 |

`ghat1` |
Expression matrix of deconvolved cell-specific gene expression estimates for group 1. |

`se1` |
Standard error group 1 |

`n1` |
Group 1 size |

`ghat2` |
Expression matrix of deconvolved cell-specific gene expression estimates for group 2. |

`se2` |
Standard error group 2 |

`n2` |
Group 2 size |

`standardize` |
Standardize contrast values, into SAM shrinked statistic. |

`medianCenter` |
Median center rhat distributions for each cell-type |

`nonNeg` |
Negative values not allowed such as in a single channel microarray. Zero them if negative (a conervative option) |

`stat.only` |
logical that indicates if the returned object should consists in the
matrix of cell type-specific SAM statistic only, or contain more detailed data about
the fit (see section |

A matrix object that contains the – standardised – contrast of the average cell-specific expression profile of the two groups, per cell-type (Size k by g where k is the number of cells and g is the number of genes).

If `stat.only=FALSE`

, then result is a list with the following elements, where
matrix elements have cell types in rows and genes in columns:

- coefficients
a matrix of cell-specific contrasts between the two groups

- se
a matrix of cell-specific standard errors

- s0
a matrix of cell-specific standard error SAM shrinkage

- stat
a matrix of – possibly median-centered – cell-specific SAM shrinked t-test statistics

- stat.med
a vector containing the medians of each cell-specific SAM shrinked t-test statistics

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,
doi: 10.1038/nmeth.1439 (URL: http://doi.org/10.1038/nmeth.1439).

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