filter_chromosome.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocess_assay.R
\name{filter_chromosome}
\alias{filter_chromosome}
\title{Filter Specific Genes on Chromosome}
\usage{
filter_chromosome(
  summarized_experiment,
  chromosome = NULL,
  ensemble_name = "ensembl_gene_id",
  df_biomart = NULL,
  use_row_range = T,
  filter_out = T
)
}
\arguments{
\item{summarized_experiment}{SummarizedExperiment or matrix like object.}

\item{chromosome}{Name of chromosomes to be filtered out | 1-24, X, Y multiple are possible}

\item{df_biomart}{Data frame containing biomaRt results}

\item{use_row_range}{Logical - Chromosome info is available in rowRanges of the SE}

\item{filter_out}{logical - If true, filters out all chromosomes stated in "chromosome", if FALSE, then only genes on said chromosomes are kept}

\item{seqnames}{Character - Name of column in rowRange containing chromosome names (not working with NSE)}
}
\value{

}
\description{
This function filters genes that are located on specific chromosomes.
}
\details{
Gene names have to be in rows and as ensembl gene IDs. e.g ENSG00000091831. If there is already a data frame with genes and their location on the chromosome, you can use that df instead.
That data frame needs to have the columns "ensembl_gene_id" and "chromosome_name".
}