RunIntLim: Run linear models and retrieve relevant statistics

In Mathelab/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 = NULL, outcome = "metabolite",
  covar = NULL, class.covar = NULL)

Arguments

inputData	MultiDataSet object (output of ReadData()) with gene expression, metabolite 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	'metabolite' or 'gene' must be set as outcome/independent variable (default is 'metabolite')
covar	Additional variables from the phenotypic data that be integrated into linear model
class.covar	Describing whether additional variables are 'numeric' or 'categorial'

Value

IntLimModel object with model results

Examples

dir <- system.file("extdata", package="IntLIM", mustWork=TRUE)
csvfile <- file.path(dir, "NCItestinput.csv")
mydata <- ReadData(csvfile,metabid='id',geneid='id')
## Not run: 
myres <- RunIntLim(mydata,stype="PBO_vs_Leukemia")

## End(Not run)

Mathelab/IntLIM documentation built on July 9, 2022, 5:10 p.m.