assay_to_model.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/assay_to_model.R
\name{assay_to_model}
\alias{assay_to_model}
\title{Gene Expression to Model Matrix}
\usage{
assay_to_model(data, assay, zscore = T, impute_na = T, fun = mean)
}
\arguments{
\item{zscore}{Logical - should the data be transformed to mean = 0 and sd = 1}

\item{impute_na}{Logical - should the missing entries be imputed by fun}

\item{fun}{function - function to impute the missing values columwise either mean or median}

\item{summarized_experiment}{A SummarizedExperiment object or a matrix.}

\item{index}{Integer - assay index of SummarizedExperiment}
}
\value{
Returns a model matrix with gene expression scaled within 0 to 1
}
\description{
This function transforms a expression matrix into a model matrix. Usable with SE or simple matrices.
}
\details{
SummarizedExperiment genes are in rows and samples in columns. In the final model matrix the samples are in rows and the predictor variables (genes) are in columns.They are transposed so when you insert a matrix, you'll have to trasnpose them beforehand.
}