extract_design.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/extract_design.R
\name{extract_design}
\alias{extract_design}
\title{Obtain design matrix (X) for variants from a mutation annotation file (maf)}
\usage{
extract_design(
  maf,
  variant_col = "variant",
  sample_id_col = "sample",
  variant_subset = NULL,
  ...
)
}
\arguments{
\item{maf}{mutation annotation file --
a data frame-like object with at least two columns containing
variant labels and sample IDs. NOTE: uniqueness of rows of maf is assumed.}

\item{variant_col}{name of the column in \code{maf} containing variant labels.}

\item{sample_id_col}{name of the column in \code{maf} containing tumor sample IDs.}

\item{variant_subset}{The subset of variant for which the design matrix
is to be constructed. Either NULL, in which case all variants present in the
maf file will be considered, or a character vector which will constitute the
column names of the output.}

\item{...}{Unused.}
}
\value{
returns an n_tumor x n_variants design matrix for
variant indicators (in dgCMatrix format)
}
\description{
Obtain design matrix (X) for variants from a mutation annotation file (maf)
}
\examples{

data("impact")
top_v <- variant_screen_mi(
  maf = impact,
  variant_col = "Variant",
  cancer_col = "CANCER_SITE",
  sample_id_col = "patient_id",
  mi_rank_thresh = 200,
  return_prob_mi = FALSE
)
var_design <- extract_design(
  maf = impact,
  variant_col = "Variant",
  sample_id_col = "patient_id",
  variant_subset = top_v
)
dim(var_design)


}