add loess normalization with reference

diff --git a/man/loess_normalization_reference.Rd b/man/loess_normalization_reference.Rd
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+++ b/man/loess_normalization_reference.Rd
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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/loess_normalization_reference.R
+\name{loess_normalization_reference}
+\alias{loess_normalization_reference}
+\title{loess_normalization_reference}
+\usage{
+loess_normalization_reference(expressions, reference = NA, iterations = 2,
+  small.positive = 0.1, sample.size = 200,
+  num.cores = max(floor(parallel::detectCores()/2), 1),
+  imputation.method = "mean", offset = 0)
+}
+\arguments{
+\item{expressions}{Gene expression values with probes in rows and samples in columns}
+
+\item{reference}{Names of rownames of reference genes}
+
+\item{iterations}{Number of iterations to run (Default: 2)}
+
+\item{small.positive}{Number to replace negative and zero expressions with (Default: 0.1).}
+
+\item{sample.size}{Number of combinations of samples to run (Default: 200).}
+
+\item{num.cores}{Number of cores to use (Default: half of them)}
+
+\item{imputation.method}{Method to impute missing values. String of "mean" (missing values are the mean of the row) or "knn" (use impute.knn to impute missing values) (Default: "mean").}
+
+\item{offset}{Offset for expression (Default: 0; set to 1 if sample contains zeros)}
+}
+\value{
+data.frame of normalized expression values
+}
+\description{
+Normalize using MvA loess using multiple processors
+}
+\details{
+For analyses where the number of samples makes all-against-all
+normalization prohibitive, this variant subselects a set of
+comparisons and runs them, iterating a specific number of times
+using as many cores as possible.
+}
+\author{
+Don Armstrong
+}
+