use_silvermantest.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocess_assay.R
\name{use_silvermantest}
\alias{use_silvermantest}
\title{Silverman Test}
\usage{
use_silvermantest(
  summarized_experiment,
  assay_index = 1,
  filter = TRUE,
  alpha = 0.05,
  p.adjust = FALSE,
  method = NULL,
  ignore_zero = TRUE,
  parallel = TRUE,
  no_cluster = NULL,
  ...
)
}
\arguments{
\item{summarized_experiment}{SummarizedExperiment or any matrix like object with rownames#'}

\item{assay_index}{Integer - index of assay of gene expression if input object is a SummarizedExperiment}

\item{filter}{Logical - filter out statistically not significant genes, threshold set by alpha}

\item{alpha}{Double - significance level}

\item{p.adjust}{Double - percentage of samples with counts greater than 0 that need to have gene counts equal or above min_value}

\item{method}{Character - methods do adjust p-values | Default = "holm"}

\item{ignore_zero}{Logical - ignore vectors with only zero values, test will throw an error otherwise}

\item{parallel}{Logical - calculation in parallel?}

\item{no_cluster}{Integer - number of clusters for parallel computation}

\item{...}{further arguments for silverman.test()}
}
\value{
If filter == F then a vector of p-values is returned, otherwise  the filtered input object
}
\description{
This function applies the \code{\link[silvermantest]{silverman.test}} on every row (gene) and if wanted already filters statistical signifcant genes.
}
\details{
p.adjust.methods:
}