1 % Generated by roxygen2 (4.1.1): do not edit by hand
2 % Please edit documentation in R/ma_loess_norm.R
3 \name{loess_normalization}
4 \alias{loess_normalization}
5 \title{loess_normalization}
7 loess_normalization(expressions, iterations = 2, small.positive = 0.1,
8 sample.size = 200, num.cores = max(floor(parallel::detectCores()/2), 1),
9 imputation.method = "mean", offset = 0)
12 \item{expressions}{Gene expression values with probes in rows and samples in columns}
14 \item{iterations}{Number of iterations to run (Default: 2)}
16 \item{small.positive}{Number to replace negative and zero expressions with (Default: 0.1).}
18 \item{sample.size}{Number of combinations of samples to run (Default: 200).}
20 \item{num.cores}{Number of cores to use (Default: half of them)}
22 \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").}
25 data.frame of normalized expression values
28 Normalize using MvA loess using multiple processors
31 For analyses where the number of samples makes all-against-all
32 normalization prohibitive, this variant subselects a set of
33 comparisons and runs them, iterating a specific number of times
34 using as many cores as possible.