methylation_beta_value.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/methylation_beta_value.R
\name{methylation_beta_value}
\alias{methylation_beta_value}
\title{Methylation Status of Probes}
\usage{
methylation_beta_value(
  annotation_cpg,
  methylation,
  cpg_name = "Composite.Element.REF",
  remove_na = 0.5,
  impute_na = T,
  margin = 0,
  fun = mean,
  shorten_colnames = T,
  int_1 = 1,
  int_2 = 12
)
}
\arguments{
\item{methylation}{RangedSummarizedExperiment - RSE containing methylation values of probes}

\item{cpg_name}{Character - Name of elementMetadata column containing the names of probes | Default = "Composite.Element.REF"}

\item{remove_na}{Double - Remove probes with more NA values than this threshold. | Remove rows with more than >remove_na< NAs}

\item{impute_na}{Logical - Impute NAs in data by mean in column? If False columns with NA are droppe}

\item{shorten_colnames}{Logical - Should the column names be shortened to match patient IDs? | Careful for duplicates}

\item{int_1}{Integer - First Integer for substr of column name}

\item{int_2}{Integer - Second Integer for substr of column name}

\item{annotated_cpg}{GRanges - Annotated cpg probes from mmRmeta::methylation_cpg_annotation}

\item{by}{Integer - impute beta values probewise (0) or patientwise (1), Default 0}
}
\value{

}
\description{
This function returns a data frame containing the beta values for the methylation probes.
}