From b72798b2e94b95c1ac713f11c16eedb7eb7895ce Mon Sep 17 00:00:00 2001
From: Martin Petr <git@bodkan.net>
Date: Wed, 8 May 2024 19:18:19 +0200
Subject: [PATCH] Remove deprecated keep_transitions

---
 NAMESPACE               |  1 -
 R/eigenstrat.R          | 17 -----------------
 man/keep_transitions.Rd | 21 ---------------------
 3 files changed, 39 deletions(-)
 delete mode 100644 man/keep_transitions.Rd

diff --git a/NAMESPACE b/NAMESPACE
index a62f713..e8457a8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,7 +11,6 @@ export(f3)
 export(f4)
 export(f4ratio)
 export(filter_bed)
-export(keep_transitions)
 export(loginfo)
 export(merge_eigenstrat)
 export(qpAdm)
diff --git a/R/eigenstrat.R b/R/eigenstrat.R
index fba4555..0a228da 100644
--- a/R/eigenstrat.R
+++ b/R/eigenstrat.R
@@ -195,23 +195,6 @@ filter_bed <- function(data, bed, remove = FALSE, outfile = tempfile(fileext = "
 
 
 
-#' Remove transversions (C->T and G->A substitutions)
-#'
-#' Remove substitutions that are more likely to be a result of ancient DNA
-#' damage (C->T and G->A substitutions).
-#'
-#' @param data EIGENSTRAT data object.
-#' @param outfile Path to an output snp file with coordinates of excluded sites.
-#'
-#' @return Updated S3 EIGENSTRAT data object with an additional 'exclude' slot
-#'     specifying the path to the set of SNPs to be removed.
-#'
-#' @export
-keep_transitions <- function(data, outfile = tempfile(fileext = ".snp")) {
-  .Deprecated("transversions_only")
-  transversions_only(data, outfile)
-}
-
 #' Remove transversions (C->T and G->A substitutions)
 #'
 #' Remove substitutions that are more likely to be a result of ancient DNA
diff --git a/man/keep_transitions.Rd b/man/keep_transitions.Rd
deleted file mode 100644
index 3100957..0000000
--- a/man/keep_transitions.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/eigenstrat.R
-\name{keep_transitions}
-\alias{keep_transitions}
-\title{Remove transversions (C->T and G->A substitutions)}
-\usage{
-keep_transitions(data, outfile = tempfile(fileext = ".snp"))
-}
-\arguments{
-\item{data}{EIGENSTRAT data object.}
-
-\item{outfile}{Path to an output snp file with coordinates of excluded sites.}
-}
-\value{
-Updated S3 EIGENSTRAT data object with an additional 'exclude' slot
-    specifying the path to the set of SNPs to be removed.
-}
-\description{
-Remove substitutions that are more likely to be a result of ancient DNA
-damage (C->T and G->A substitutions).
-}