makeLogFCs: Calculate log fold changes and associated p-values.
In stevehoang/assayr: Tools for analyzing biochemical assay data.

Description Usage Arguments Value Examples

Wrapper for calculating fold changes based on multcomp::glht() object.

1	makeLogFCs(ht, base = 10, round_to = 2, conf_level = 0.95)

`ht`	An object of class "glht" from `multcomp::glht`.
`base`	A numeric value specifying the log based used in the model. Default is 10.
`round_to`	A numeric value specifying the number of decimal places in percent change columns in result.
`conf_level`	A numeric value between 0 and 1 for confidence level. Default is .95.

A data frame with est (estimate change), lwr, upr (confidence bounds), contrast (predictor levels being compared), pct_label (text, for plotting labels), pct_fill (numeric, for plotting scales), and a p-value adjusted for multiple comparrisons but multcomp::glht.

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mod <- lm(Sepal.Length ~ 0 + Species, data = iris) # use model with intercept set to 0
ht <- multcomp::glht(mod, linfct = mcp(Species = "Dunnet"))
fcs <- makeLogFCs(ht)