compute_models_with_limma: Compute lipid-specific regression models
In lipidomeR: Integrative Visualizations of the Lipidome

Description Usage Arguments Value See Also

View source: R/compute_models_with_limma.R

Use this function to computing multiple regression models that can be directly supplied to the visualization functions of the 'lipidomeR'.

compute_models_with_limma(
  x,
  dependent.variables,
  independent.variables,
  random.effect = NULL,
  formula = NULL,
  F.test = FALSE,
  print.table1 = FALSE,
  scale.dependent.variables = TRUE,
  scale.independent.variables = FALSE,
  verbose = TRUE
)

`x`	(Required) data matrix.
`dependent.variables`	(Required) vector of names of dependent variables. These should be the names of the lipids.
`independent.variables`	(Required) vector of names of the independent variables. These should be the names of the variables defining the experiment design.
`random.effect`	(Optional) name of a single variable specifying the random effect for a random-effects model. For instance, `ID` specifies a random effect as in `limma::duplicateCorrelation( ..., block = x$'ID' )`.
`formula`	(Optional) character string of model formula in the format accepted by the function `model.matrix` and starting with `~`. Variables mentioned in the formula should be included in the `independent.variables` argument. For instance, `Group * Treatment`.
`F.test`	(Optional) `TRUE` or `FALSE`: Should an F-test for analysis of variance (ANOVA) or analysis of covariance (ANCOVA) be computed?
`print.table1`	(Optional) `TRUE` or `FALSE`: Should a summary table of the independent variables be printed?
`scale.dependent.variables`	(Optional) `TRUE` or `FALSE`: Should dependent variables be scaled to zero-mean and unit-variance prior to model fitting?
`scale.independent.variables`	(Optional) `TRUE` or `FALSE`: Should independent variables be scaled to zero-mean and unit-variance prior to model fitting?
`verbose`	(Optional) `TRUE` or `FALSE`: Print messages from the model fitting?

List of regression results the that can be directly supplied as an argument to the function heatmap_lipidome_from_limma and other visualization functions of the lipidomeR.

heatmap_lipidome_from_limma for visualizing the output of this function.

lipidomeR documentation built on March 26, 2020, 5:32 p.m.