Description Usage Arguments Details Value Examples

ABSDataSet object and constructors

1 2 3 | ```
ABSDataSet(counts, groups, normMethod = c("user", "qtotal", "total", "quartile",
"geometric", "TMM"), sizeFactor = 0, paired = FALSE, minDispersion = NULL, minRates = 0.1,
maxRates = 0.3, LevelstoNormFC = 100)
``` |

`counts` |
a matrix or table with at least two columns and one row, |

`groups` |
a factor with two groups, whose length should be equal with sample size |

`normMethod` |
method for estimating the size factors, should be one of 'user', 'qtotal', 'total', 'quartile', 'geometric' and 'TMM'. See |

`sizeFactor` |
size factors for 'user' method, self-defined size factors by user. |

`paired` |
switch for differential expression detection in paired samples. |

`minDispersion` |
a positive double for user-defined penalty of dispersion estimation |

`minRates` |
low bounder rate of baseline estimation for counts difference, default is 0.1 |

`maxRates` |
up bounder rate of baseline estimation for counts difference, default is 0.3. Setting minRates equal with maxRates will result in a testing on user-define rate, |

`LevelstoNormFC` |
maximal level of average standard deviation in fold-change normalization according to expression level, default is 100. |

The function contructs an ABSDataSet object with counts table and groups. It also checks the structure of counts and groups.The ABSDataSet is a class, used to store the input values, intermediate calculations and results of an analysis of differential expression. It also contains information for the running time of an analysis.

An ABSDataSet object.

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