RunIntLim: Run linear models and retrieve relevant statistics

In IntLIM: Integration of Omics Data Using Linear Modeling

Run linear models and retrieve relevant statistics

Description

Run linear models and retrieve relevant statistics

Usage

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

Arguments

inputData	Named list (output of FilterData()) with analyte abundances, 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 or not to print warnings. If TRUE, do not print.

Value

IntLimResults object with model results

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