From 90800058b35fce52bec810205424db4840b58201 Mon Sep 17 00:00:00 2001
From: Liam Fitzstevens <71883978+liamfitzstevens@users.noreply.github.com>
Date: Tue, 20 Aug 2024 18:42:27 -0400
Subject: [PATCH] Update mg_profiling.R

---
 R/mg_profiling.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/mg_profiling.R b/R/mg_profiling.R
index f94cc45..079352e 100644
--- a/R/mg_profiling.R
+++ b/R/mg_profiling.R
@@ -27,14 +27,14 @@ read_bracken = function(infile, nrows=Inf, keep_frac=TRUE,
   }
   dt = data.table::fread(infile, sep='\t', nrows=nrows, check.names=TRUE,
                          nThread=nThread, ...) %>%
-    tidytable::select.(-taxIDs, -ends_with(!!to_rm)) %>%
-    tidytable::mutate.(taxonomy = gsub(';[pcofgs]__', ';', taxonomy),
+    tidytable::select(-taxIDs, -ends_with(!!to_rm)) %>%
+    tidytable::mutate(taxonomy = gsub(';[pcofgs]__', ';', taxonomy),
                        taxonomy = gsub('^d__', '', taxonomy)) %>%
-    tidytable::separate.(taxonomy, tax_levs, sep=';') %>%
-    tidytable::pivot_longer.(cols=ends_with(!!to_keep),
+    tidytable::separate(taxonomy, tax_levs, sep=';') %>%
+    tidytable::pivot_longer(cols=ends_with(!!to_keep),
                                names_to='Sample',
                                values_to='Abundance') %>%
-    tidytable::mutate.(Sample = gsub('(_frac|_num)$', '', Sample))
+    tidytable::mutate(Sample = gsub('(_frac|_num)$', '', Sample))
 
   return(dt)
 }