fitMultipleTimeSeries: Discover differentially abundant time intervals for all...

Description Usage Arguments Value See Also Examples

View source: R/fitTimeSeries.R

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

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

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.

featureOrder

Hierarchy of levels in taxonomy as fData colnames

...

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:

See Also

cumNorm fitSSTimeSeries fitTimeSeries

Examples

1
2
3
data(mouseData)
res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class="status",
          id="mouseID",time="relativeTime",B=1)

metagenomeSeq documentation built on May 20, 2017, 9:57 p.m.

Search within the metagenomeSeq package
Search all R packages, documentation and source code