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