Calculate time intervals of interest using SS-Anova fitted models. Fitting is performed uses Smoothing Spline ANOVA (SS-Anova) to find interesting intervals of time. Given observations at different time points for two groups, fitSSTimeSeries calculates a function that models the difference in abundance between two groups across all time. Using permutations we estimate a null distribution of areas for the time intervals of interest and report significant intervals of time. Use of the function for analyses should cite: "Finding regions of interest in high throughput genomics data using smoothing splines" Talukder H, Paulson JN, Bravo HC. (In preparation)

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`obj` |
metagenomeSeq MRexperiment-class object. |

`formula` |
Formula for ssanova. Of the form: abundance ~ ... where ... includes any pData slot value. |

`feature` |
Name or row of feature of interest. |

`class` |
Name of column in phenoData of MRexperiment-class object for class memberhip. |

`time` |
Name of column in phenoData of MRexperiment-class object for relative time. |

`id` |
Name of column in phenoData of MRexperiment-class object for sample id. |

`lvl` |
Vector or name of column in featureData of MRexperiment-class object for aggregating counts (if not OTU level). |

`include` |
Parameters to include in prediction. |

`C` |
Value for which difference function has to be larger or smaller than (default 0). |

`B` |
Number of permutations to perform |

`norm` |
When aggregating counts to normalize or not. |

`log` |
Log2 transform. |

`sl` |
Scaling value. |

`...` |
Options for ssanova |

List of matrix of time point intervals of interest, Difference in abundance area and p-value, fit, area permutations, and call.

A list of objects including:

timeIntervals - Matrix of time point intervals of interest, area of differential abundance, and pvalue.

data - Data frame of abundance, class indicator, time, and id input.

fit - Data frame of fitted values of the difference in abundance, standard error estimates and timepoints interpolated over.

perm - Differential abundance area estimates for each permutation.

call - Function call.

`cumNorm`

`ssFit`

`ssIntervalCandidate`

`ssPerm`

`ssPermAnalysis`

`plotTimeSeries`

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