A function called in SimData used to trim and sort the matrix of counts provided.

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`counts` |
A matrix of counts where each row specifies a gene and each column specifies a replicate. |

`treatment` |
A vector specifying the treatment group for each column of the counts matrix. Only two treatment groups of either paired or unpaired data are allowed. |

`replic` |
A vector specifying the replicate for each column of the counts matrix when there is paired data; optional if data is unpaired. |

`sort.method` |
Character vector specifying one of "unpaired" or "paired", depending on the structure of the data. |

`norm.factors` |
An optional positive numeric vector of multiplicative normalization factors for each column of the counts matrix. |

List containing:

`counts` |
sorted and trimmed matrix of counts. |

`replic` |
sorted and trimmed replic vector. |

`treatment` |
sorted and trimmed treatment vector. |

`norm.factors` |
sorted and trimmed offset vector. |

`sorting` |
sorting vector used to sort and trim. |

Samuel Benidt <sgbenidt@gmail.com>

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