pmartRseq_aldex2: Modified version of ALDEx2 for pmartRseq
In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description Usage Arguments Details Value Author(s) References

This function calculates the centered-log ratio with draws from a Dirichlet distribution and runs a liner or linear mixed-effects model

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pmartRseq_aldex2(omicsData, mainEffects = NULL, mc.samples = 128,
  denom = "all", verbose = FALSE, interactions = FALSE,
  randomEffect = NULL, pval_thresh = 0.05)

`omicsData`	an object of the class 'seqData' reated by `as.seqData`.
`mainEffects`	Optional, a character vector detailing which factors should be used as main effects in the model. The variable name must match a column name from `omicsData$f_data`. If NULL, will use the same main effects that were used in `group_designation`.
`mc.samples`	The number of Monte Carlo instances to use. Default is 128.
`denom`	Character vector indicating which features to use as the denominator for the geometric mean. Default is "all".
`verbose`	Print diagnostic information while running. Default is FALSE.
`interactions`	Logical, indicating whether or not interactions should be considered in the model. If TRUE, all possible interactions will be used. If FALSE, none will be used.
`randomEffect`	Optional, character specifying which factor to use as a random effect in the model. This will be used in the form (1\|randomEffect). Must match a column name from `omicsData$f_data`

Modified version of ALDEx2, allowing for multiple factors and random effects

An object of class paRes (also a list) containing to parts - clr, the clr transformed values for each Monte-Carlo Dirichlet instance, and res, a data frame with a p.value, statistic, degrees of freedom, and sum of squares values for each feature and each term in the mdoel.

Allison Thompson

Fernandes, Unifying...

pmartR/pmartRseq documentation built on May 25, 2019, 9:20 a.m.