From 5ab5407366d5e95b43e6909ecd4261ca568ad532 Mon Sep 17 00:00:00 2001
From: teng-gao <tgaoteng@gmail.com>
Date: Tue, 6 Jun 2023 12:08:51 -0400
Subject: [PATCH] solve cran note S3 method mismatch

---
 R/utils.R          |  4 ++--
 man/t.test.pval.Rd | 12 ------------
 2 files changed, 2 insertions(+), 14 deletions(-)
 delete mode 100644 man/t.test.pval.Rd

diff --git a/R/utils.R b/R/utils.R
index 893d122d..0b792af5 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1236,7 +1236,7 @@ find_common_diploid = function(
             bind_rows() %>%
             rowwise() %>%
             mutate(
-                p = t.test.pval(
+                p = t_test_pval(
                     x = bulks_bal$lnFC[bulks_bal$seg == i & bulks_bal$sample == s],
                     y = bulks_bal$lnFC[bulks_bal$seg == j & bulks_bal$sample == s]
                 ),
@@ -1853,7 +1853,7 @@ simes_p = function(p.vals, n_dim) {
 
 #' T-test wrapper, handles error for insufficient observations
 #' @keywords internal
-t.test.pval = function(x, y) {
+t_test_pval = function(x, y) {
     if (length(x) <= 1 | length(y) <= 1) {
         return(1)
     } else {
diff --git a/man/t.test.pval.Rd b/man/t.test.pval.Rd
deleted file mode 100644
index 7cee0790..00000000
--- a/man/t.test.pval.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{t.test.pval}
-\alias{t.test.pval}
-\title{T-test wrapper, handles error for insufficient observations}
-\usage{
-\method{t.test}{pval}(x, y)
-}
-\description{
-T-test wrapper, handles error for insufficient observations
-}
-\keyword{internal}