From ca31b446754842f0ae3178e78ce80b2cc52cd97d Mon Sep 17 00:00:00 2001
From: Art Eschenlauer <esch0041@umn.edu>
Date: Mon, 16 Dec 2019 19:38:52 -0600
Subject: [PATCH] adjusted docs

---
 inst/NEWS                    | 2 +-
 vignettes/w4mclassfilter.Rmd | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/inst/NEWS b/inst/NEWS
index 2450bc0..327aa16 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -4,7 +4,7 @@
 
 * Enhancement https://github.com/HegemanLab/w4mclassfilter/issues/6 - "compute center for each treatment"
 * Built with R 3.6.1 (2019-07-05) "Action of the Toes"
-
+* Built with the command `R CMD build w4mclassfilter` to assure that vignettes are built as intended.
 
 # CHANGES IN VERSION 0.98.14
 
diff --git a/vignettes/w4mclassfilter.Rmd b/vignettes/w4mclassfilter.Rmd
index d20c8eb..c37da69 100644
--- a/vignettes/w4mclassfilter.Rmd
+++ b/vignettes/w4mclassfilter.Rmd
@@ -14,11 +14,11 @@ output:
     fig_caption: yes
 vignette: >
   %\VignetteIndexEntry{Filter W4M data by sample class}
-  %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
   \usepackage[all]{nowidow}
   \widowpenalty10000
   \clubpenalty10000
+  %\VignetteEngine{knitr::rmarkdown}
 ---
 
 ### Purpose of the `w4mclassfilter` package
@@ -48,6 +48,7 @@ or to address several data issues that may impede downstream statistical analysi
   - The column for sorting `variableMetadata` or `sampleMetadata` may be specified or defaults to the first column.
 - By default, the name of the first column `sampleMetadata` is set to `"sampleMetadata"`.
 - The name of the first column `variableMetadata` is set to `"variableMetadata"`.
+- An advanced option enables producing a "center" for each treatment in lieu of the samples for each treatment.
 
 ### How the `w4m_filter_by_sample_class` function is used
 
@@ -309,4 +310,4 @@ To support XCMS outside the context of Galaxy, `w4mclassfilter::w4m_filter_by_sa
 - "centroid" - Return only treatment-centers computed for each treatment as the mean intensity for each feature.
 - "median" - Return only treatment-centers computed for each treatment as the median intensity for each feature.
 - "medoid" - Return only treatment-centers computed for each treatement as the sample most similar to the other samples, using distances computed in principal-components space.
-- "none" - Return all samples; do not computing centers
+- "none" - Return all samples; do not computing centers.