Description Usage Arguments Details Value Note Examples

Using NB distribution to calculate p-value for each gene as well as adjust p-value

1 |

`object` |
an |

`adjmethod` |
the method for adjusting p-value, default is 'BH'. For details, see |

`useaFold` |
switch for DE detection through fold-change, which will use a normal distribution (N(0,sd)) to test the significance of log2 fold-change. The sd is estimated through a quantile function of gamma distribution at |

This function firstly calls p-value used `pnbinom`

to call pvalue based on sum of counts difference between two
groups or used `pnorm`

to call pvalue via log2 fold-change, then adjusts the pvalues via `p.adjust`

method. In addition, it also shrink the log2 fold-change towards a common dispersion
after pvalue calling.

an `ABSDataSet`

object with additional elements: shrinked log2 fold-change, pvalue and adjusted p-value,
denoted by foldChange pvalue and adj-pvalue, respectively. Use the `results`

method to get access it.

this function should run after `callParameter`

1 2 3 4 5 6 | ```
data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- callParameter(obj)
obj <- callDEs(obj)
head(results(obj))
``` |

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