From a18f5c7b255a2d6f075e3923702101812bbac3b1 Mon Sep 17 00:00:00 2001
From: Jean-Philippe Fortin <fortin946@gmail.com>
Date: Sat, 27 Aug 2022 09:15:14 -0700
Subject: [PATCH] Removed filterSpacers

---
 DESCRIPTION         | 6 +++---
 README.Rmd          | 3 +--
 README.md           | 5 ++---
 vignettes/intro.Rmd | 3 +--
 4 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ce06197..04c068d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: crisprViz
 Title: Visualization Functions for CRISPR gRNAs
-Version: 0.99.20
+Version: 0.99.21
 Authors@R: c(
     person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")),
     person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut"))
@@ -42,5 +42,5 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.1
 VignetteBuilder: knitr
-BugReports: https://github.com/Jfortin1/crisprViz/issues
-URL: https://github.com/Jfortin1/crisprViz
+BugReports: https://github.com/crisprVerse/crisprViz/issues
+URL: https://github.com/crisprVerse/crisprViz
diff --git a/README.Rmd b/README.Rmd
index 3630d49..ccb1f5b 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -256,8 +256,7 @@ Some of our candidate gRNAs target repeat elements and likely target a large num
 ```{r}
 filteredGuideSet <- crisprDesign::removeRepeats(mmp7GuideSet,
                                                 gr.repeats=repeats)
-filteredGuideSet <- crisprDesign::filterSpacers(filteredGuideSet,
-                                                criteria=list(hasSNP=FALSE))
+filteredGuideSet <- filteredGuideSet[!filteredGuideSet$hasSNP]
 plotGuideSet(filteredGuideSet,
              geneModel=mmp7GeneModel,
              targetGene="MMP7",
diff --git a/README.md b/README.md
index 502dab8..fb2f58a 100644
--- a/README.md
+++ b/README.md
@@ -348,8 +348,7 @@ remove these gRNAs and regenerate the plot.
 ``` r
 filteredGuideSet <- crisprDesign::removeRepeats(mmp7GuideSet,
                                                 gr.repeats=repeats)
-filteredGuideSet <- crisprDesign::filterSpacers(filteredGuideSet,
-                                                criteria=list(hasSNP=FALSE))
+filteredGuideSet <- filteredGuideSet[!filteredGuideSet$hasSNP]
 plotGuideSet(filteredGuideSet,
              geneModel=mmp7GeneModel,
              targetGene="MMP7",
@@ -493,7 +492,7 @@ sessionInfo()
     ## [8] base     
     ## 
     ## other attached packages:
-    ##  [1] crisprViz_0.99.18                 crisprDesign_0.99.132            
+    ##  [1] crisprViz_0.99.18                 crisprDesign_0.99.134            
     ##  [3] crisprBase_1.1.5                  BSgenome.Hsapiens.UCSC.hg38_1.4.4
     ##  [5] BSgenome_1.65.2                   rtracklayer_1.57.0               
     ##  [7] Biostrings_2.65.2                 XVector_0.37.0                   
diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd
index 8e85294..0fb1d4c 100644
--- a/vignettes/intro.Rmd
+++ b/vignettes/intro.Rmd
@@ -316,8 +316,7 @@ remove these gRNAs and regenerate the plot.
 ```{r}
 filteredGuideSet <- crisprDesign::removeRepeats(mmp7GuideSet,
                                                 gr.repeats=repeats)
-filteredGuideSet <- crisprDesign::filterSpacers(filteredGuideSet,
-                                                criteria=list(hasSNP=FALSE))
+filteredGuideSet <- filteredGuideSet[!filteredGuideSet$hasSNP]
 plotGuideSet(filteredGuideSet,
              geneModel=mmp7GeneModel,
              targetGene="MMP7",