Removed filterSpacers

crisprVerse · Aug 27, 2022 · a18f5c7 · a18f5c7
1 parent cee850e
commit a18f5c7
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Showing 4 changed files with 7 additions and 10 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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",