From 6c0b8872d3b0c1d9143441fc364319c4547c274e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Mon, 28 Oct 2024 10:17:56 -0400
Subject: [PATCH] updates

---
 DESCRIPTION        | 8 --------
 R/bam_to_counts.R  | 2 +-
 man/calc_counts.Rd | 4 ++--
 3 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6737884..ba7285a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,16 +13,8 @@ License: GPL-3
 URL: https://github.com/FredHutch/gimap
 BugReports: https://github.com/FredHutch/gimap/issues
 Imports:
-    readr,
     dplyr,
-    tidyr,
     knitr,
-    rmarkdown,
-    ggplot2,
-    magrittr,
-    kableExtra,
-    pheatmap,
-    purrr,
     utils,
     stats,
     stringr,
diff --git a/R/bam_to_counts.R b/R/bam_to_counts.R
index 1a5feef..88a4a46 100755
--- a/R/bam_to_counts.R
+++ b/R/bam_to_counts.R
@@ -1,7 +1,7 @@
 #' Obtain the counts for a group of samples
 #' @description This function takes a forward and reverse bam files for a group of samples and returns the counts and stats.
 #' @param bam_dir a file path to a directory where the bam files associated with the sample names will be stored. 
-#' @param sample_name a character vector that indicates the name of the samples as they are listed in the file names. 
+#' @param sample_names a character vector that indicates the name of the samples as they are listed in the file names. 
 #' @param time TRUE/FALSE you want the duration this takes to run printed out
 #' @importFrom furrr future_pmap future_map 
 #' @importFrom purrr reduce
diff --git a/man/calc_counts.Rd b/man/calc_counts.Rd
index 0f06d2d..6c01310 100644
--- a/man/calc_counts.Rd
+++ b/man/calc_counts.Rd
@@ -9,9 +9,9 @@ calc_counts(bam_dir, sample_names, time = TRUE)
 \arguments{
 \item{bam_dir}{a file path to a directory where the bam files associated with the sample names will be stored.}
 
-\item{time}{TRUE/FALSE you want the duration this takes to run printed out}
+\item{sample_names}{a character vector that indicates the name of the samples as they are listed in the file names.}
 
-\item{sample_name}{a character vector that indicates the name of the samples as they are listed in the file names.}
+\item{time}{TRUE/FALSE you want the duration this takes to run printed out}
 }
 \description{
 This function takes a forward and reverse bam files for a group of samples and returns the counts and stats.