filter_rare.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocess_assay.R
\name{filter_rare}
\alias{filter_rare}
\title{Filter Infrequently Expressed Genes}
\usage{
filter_rare(
  summarized_experiment,
  assay_index = 1,
  threshold = 0.05,
  min_counts = 5,
  min_percentage = 0.1,
  verbose = T
)
}
\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{threshold}{Double - minimum percentage of expression values of a gene that are higher than 0}

\item{min_counts}{Integer - minimum value of gene counts}

\item{min_percentage}{Double - percentage of samples with counts greater than 0 that need to have gene counts equal or above min_value}
}
\value{
SummarizedExperiment with probably less genes than before
}
\description{
This function filters genes that are expressed distinguished by a given percentage. Less expressed than minimum percentage
}
\details{
The Arguments min_counts and min_percentage allow for a more strict filtering. One is able to exclude genes with small expression values.
}
\examples{
filteredBreastBRCA <- filter_rare(breastBRCA, assay_index = 1, threshold = 0.10, min_counts = 5, min_percentage = 0.20)
#All genes with more than 90\% of samples having zero counts are excluded. Moreover, only genes with 20\% of their samples having expression counts greater than 5 are kept.
}