label_mutations.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/label_mutations.R
\name{label_mutations}
\alias{label_mutations}
\alias{label_mutations.ref_alt_cov_tbl}
\title{Label mutations}
\usage{
label_mutations(.data, .before = NULL, .after = NULL)

\method{label_mutations}{ref_alt_cov_tbl}(.data, .before = NULL, .after = NULL)
}
\arguments{
\item{.data}{The data set containing REF and ALT calls.}

\item{.before, .after}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
<\code{\link[=dplyr_tidy_select]{tidy-select}}> Optionally, control where new columns
should appear (the default is to add to the right-hand side). See
\code{\link[dplyr:relocate]{dplyr::relocate()}} for more details.}
}
\value{
The object \code{.data} with an added column that indicates the mutation type of
each row. The column is added to the right-hand side by default, but this may
be controlled by the \code{.before} and \code{.after} arguments.
}
\description{
For each data point, label a mutation as \code{"ref"}, \code{"alt"}, \code{"ins"}, or
\code{"del"}.
\itemize{
\item Data points that have more reference (REF) than alternate (ALT) calls will
be labeled as \code{"ref"}.
\item Mutations whose REF and ALT calls are both one base pair and who have more
ALT calls than REF calls will be labeled as \code{"alt"}.
\item Mutations whose REF and ALT calls differ in length and have more ALT calls
than REF calls will be labeled as \code{"ins"}.
\item Mutations whose REF and ALT calls differ in length and have more REF calls
than ALT calls will be labeled as \code{"del"}.
}
}
\examples{
# Read example data
data <- read_tbl_ref_alt_cov(
  miplicorn_example("reference_AA_table.csv"),
  miplicorn_example("alternate_AA_table.csv"),
  miplicorn_example("coverage_AA_table.csv"),
  gene == "atp6"
)

# Add ref and alt calls to data
sequences <- c("A", "T", "C", "G", "AT", "TC", "TGC")
data <- dplyr::mutate(
  data,
  ref = sample(sequences, size = nrow(data), replace = TRUE),
  alt = sample(sequences, size = nrow(data), replace = TRUE)
)

# Label the mutations
label_mutations(data)
label_mutations(data, .after = alt)
}