run.feature.lm: Runs a linear model for a single given phenotypic feature

Description Usage Arguments

Description

This function is a wrapper for limma::lmFit, which is usually used to run linear models for microarray data. It returns a dataframe with the t-statistic, p-value, and FDR adjusted p-value for each gene.

Usage

1
run.feature.lm(feature.name, pheno.data, dataset, is.numeric = TRUE)

Arguments

feature.name

A string of the column name in the phenotype data matrix corresponding to the feature of interest

pheno.data

The full phenotypic data matrix (e.g. pData(expression.set))

dataset

the expression matrix of interest. ncol(dataset) should == nrow(pheno.data)

is.numeric

Whether the feature in question is numeric or not. If not numeric, it's assumed to be a factor.


definitelysean/sgaphd documentation built on May 15, 2019, 3:20 a.m.