use_diptest.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocess_assay.R
\name{use_diptest}
\alias{use_diptest}
\title{DipTest}
\usage{
use_diptest(
  summarized_experiment,
  assay_index = 1,
  filter = TRUE,
  alpha = 0.05,
  ignore_zero = TRUE,
  ignore_percentage = 0.2,
  ignore_threshold = NULL,
  p.adjust = FALSE,
  method = NULL,
  parallel = TRUE,
  no_cluster = NULL,
  ...
)
}
\arguments{
\item{summarized_experiment}{SummarizedExperiment or any data frame like object.}

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

\item{filter}{Logical - filter input data by alpha}

\item{alpha}{Double - significance level | p-values equal or below alpha are kept}

\item{ignore_zero}{Logical - ignore zero values}

\item{p.adjust}{Logical - use p.adjust}

\item{method}{Character - method used in p.adjust}

\item{parallel}{Logical - use parallel computation of test}

\item{no_cluster}{Integer - number of clusters used in parallelization | Default (number of cores - 1)}

\item{...}{further arguments for diptest(B)}
}
\value{
Returns either a vector of pValues or a filtered input object.
}
\description{
This function applies the silvermantest on every row (gene)
}
\details{
When applying the test on data with many zero values, the test most likely will be significant anyway. Those zero values are excluded from the diptest. But you can set set an expection with "..:". Meaning that when there are zero values but a percentage of samples
is above a certain value ":::" then the diptest is applied on the whole data set.
If filter is set to TRUE the function returns an object with the same class as summarized_experiment. Otherwise a vector of p-values is returned.
}