Discover differentially abundant time intervals for all bacteria

Description

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

Usage

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fitMultipleTimeSeries(obj, lvl = NULL, B = 1, ...)

Arguments

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.

...

Options for fitTimeSeries, except feature.

Value

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.

See Also

cumNorm fitSSTimeSeries fitTimeSeries

Examples

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data(mouseData)
res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class="status",
          id="mouseID",time="relativeTime",B=1)

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