plotOrd
(Package: metagenomeSeq) :
Plot of either PCA or MDS coordinates for the distances of normalized or unnormalized counts.
This function plots the PCA / MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.
● Data Source:
BioConductor
● Keywords:
● Alias: plotOrd
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1 images
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This function plots the number of observed features vs. the depth of coverage.
● Data Source:
BioConductor
● Keywords:
● Alias: plotRare
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1 images
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plotTimeSeries
(Package: metagenomeSeq) :
Plot difference function for particular bacteria
Plot the difference in abundance for significant features.
● Data Source:
BioConductor
● Keywords:
● Alias: plotTimeSeries
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1 images
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posteriorProbs
(Package: metagenomeSeq) :
Access the posterior probabilities that results from analysis
Accessing the posterior probabilities following a run through fitZig
● Data Source:
BioConductor
● Keywords:
● Alias: posteriorProbs, posteriorProbs,MRexperiment-method
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0 images
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Function to check if object is a MRexperiment class or matrix
● Data Source:
BioConductor
● Keywords:
● Alias: returnAppropriateObj
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0 images
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ssFit
(Package: metagenomeSeq) :
smoothing-splines anova fit
Sets up a data-frame with the feature abundance, class information, time points, sample ids and returns the fitted values for the fitted model.
● Data Source:
BioConductor
● Keywords:
● Alias: ssFit
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Calculates time intervals of interest using SS-Anova fitted confidence intervals.
● Data Source:
BioConductor
● Keywords:
● Alias: ssIntervalCandidate
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0 images
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ssPerm
(Package: metagenomeSeq) :
class permutations for smoothing-spline time series analysis
Creates a list of permuted class memberships for the time series permuation tests.
● Data Source:
BioConductor
● Keywords:
● Alias: ssPerm
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0 images
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ssPermAnalysis
(Package: metagenomeSeq) :
smoothing-splines anova fits for each permutation
Calculates the fit for each permutation and estimates the area under the null (permutted) model for interesting time intervals of differential abundance.
● Data Source:
BioConductor
● Keywords:
● Alias: ssPermAnalysis
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0 images
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trapz
(Package: metagenomeSeq) :
Trapezoidal Integration
Compute the area of a function with values 'y' at the points 'x'. Function comes from the pracma package.
● Data Source:
BioConductor
● Keywords:
● Alias: trapz
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0 images
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providing 
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