Description Usage Arguments Value See Also Examples

View source: R/fitTimeSeries.R

Calculate time intervals of significant differential abundance over all bacteria of a particularly specified level (lvl). If not lvl is specified, all OTUs are analyzed. Warning, function can take a while

1 | ```
fitMultipleTimeSeries(obj, lvl = NULL, B = 1, featureOrder = NULL, ...)
``` |

`obj` |
metagenomeSeq MRexperiment-class object. |

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

`B` |
Number of permutations to perform. |

`featureOrder` |
Hierarchy of levels in taxonomy as fData colnames |

`...` |
Options for |

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

A list of lists for which each includes:

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`

`fitSSTimeSeries`

`fitTimeSeries`

1 2 3 |

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