From f6625b45d24b67f862b46f6bef24bc1540366d92 Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Tue, 31 Oct 2023 07:43:53 +0100
Subject: [PATCH] minor bug in clustered_seqs var call
---
NAMESPACE | 2 ++
R/variant_classifier.R | 5 +++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/NAMESPACE b/NAMESPACE
index 019a2b6..84885ea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -45,7 +45,9 @@ export(translate_and_count_stops)
export(variant_classifier)
export(veganify_asvcounts)
export(veganify_generic_wide_tbl)
+import(Biostrings)
import(DECIPHER)
+import(DNAStringSetList)
import(dplyr)
import(forcats)
import(ggplot2)
diff --git a/R/variant_classifier.R b/R/variant_classifier.R
index dda8133..4eafec8 100644
--- a/R/variant_classifier.R
+++ b/R/variant_classifier.R
@@ -8,6 +8,7 @@
#'
#' @return A modified master table with variant classifications
#' @import dplyr purrr stringr tibble tidyr
+#' @import Biostrings DNAStringSetList
#' @export
variant_classifier <- function(
@@ -26,8 +27,8 @@ variant_classifier <- function(
# Create a table for clustered sequences and filter out clusters with only one sequence
clustab_tbl <- cluster_tbl_named(clustered_sequences) %>%
- left_join(tibble(seqnames = unlist(map(clustered_seqs, names)),
- seqs = as.character(unlist(clustered_sequences))),
+ left_join(tibble(seqnames = unlist(map(clustered_sequences, names)),
+ seqs = as.character(Biostrings:: unlist(clustered_sequences))),
by = 'seqnames') %>%
dplyr::filter(clus_size > 1)
--
GitLab