RunIntLimAllFolds: Run linear models for all data folds. This is a wrapper to...

In IntLIM: Integration of Omics Data Using Linear Modeling

Run linear models for all data folds. This is a wrapper to RunIntLim.

Description

Run linear models for all data folds. This is a wrapper to RunIntLim.

Usage

RunIntLimAllFolds(
  inputData,
  stype = "",
  outcome = 1,
  covar = c(),
  continuous = FALSE,
  save.covar.pvals = FALSE,
  independent.var.type = 1,
  remove.duplicates = FALSE,
  suppressWarnings = FALSE
)

Arguments

inputData	IntLimData object (output of ReadData()) with analyte levels and associated meta-data
stype	column name that represents sample type (by default, it will be used in the interaction term). Only 2 categories are currently supported.
outcome	'1' or '2' must be set as outcome/independent variable (default is '1')
covar	Additional variables from the phenotypic data that be integrated into linear model
continuous	boolean to indicate whether the data is continuous or discrete
save.covar.pvals	boolean to indicate whether or not to save the p-values of all covariates, which can be analyzed later but will also lengthen computation time. The default is FALSE.
independent.var.type	'1' or '2' must be set as independent variable (default is '1')
remove.duplicates	boolean to indicate whether or not to remove the pair with the highest p-value across two duplicate models (e.g. m1~m2 and m2~m1)
suppressWarnings	whether to suppress warnings

Value

List of IntLimModel objects with model results

IntLIM documentation built on Aug. 22, 2022, 5:05 p.m.