IntLIM (version 2.0.2)

RunIntLim: 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
)

Value

IntLimResults object with model results

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.