From 94f36c49f082ab351182456713beea8c5a4074d1 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Fri, 7 Apr 2017 14:07:38 -0500 Subject: [PATCH] add loess normalization with reference --- man/loess_normalization_reference.Rd | 44 ++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 man/loess_normalization_reference.Rd diff --git a/man/loess_normalization_reference.Rd b/man/loess_normalization_reference.Rd new file mode 100644 index 0000000..34b72cd --- /dev/null +++ b/man/loess_normalization_reference.Rd @@ -0,0 +1,44 @@ +% 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 +} + -- 2.39.2