9.17_vignette

GilbertHan1011 · Sep 17, 2024 · baddfc0 · baddfc0
1 parent 4332a84
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,10 @@ Suggests:
     knitr,
     rmarkdown,
     testthat,
-    GenomicInteractions
+    TxDb.Hsapiens.UCSC.hg38.knownGene,
+    org.Hs.eg.db,
+    Txdb.Mm.UCSC.mm10.knownGene,
+    org.Mm.eg.db
 Collate: class.R AllGenerics.R getset.R
         methods.R annotate.R distance.R formatConverter.R 
         linkSet-package.R GRange_method.R test_helper.R

diff --git a/docs/articles/linkSet.html b/docs/articles/linkSet.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   hic_workthrough: hic_workthrough.html
   linkSet: linkSet.html
-last_built: 2024-09-17T14:18Z
+last_built: 2024-09-17T14:28Z
 urls:
   reference: https://gilberthan1011.github.io/linkSet/reference
   article: https://gilberthan1011.github.io/linkSet/articles
diff --git a/docs/reference/annotatePromoter-linkSet-method.html b/docs/reference/annotatePromoter-linkSet-method.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -2,20 +2,33 @@
 <url><loc>https://gilberthan1011.github.io/linkSet/404.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/LICENSE-text.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/LICENSE.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/articles/hic_workthrough.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/articles/index.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/articles/linkSet.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/authors.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/index.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/Convert.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/annotateInter-linkSet-method.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/annotatePromoter-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/as.data.frame-linkSet-method.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/baitGInteractions-GInteractions-GRanges-GRanges-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/countInteractions-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/crossGeneEnhancer-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/diagnoseLinkSet-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/filterLinks-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/geom_linkset-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/geom_range.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/index.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet-GRange-Methods.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet-accessors.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet-class.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet-package.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet-subset-methods.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/linkSet.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/orderLinks-linkSet-method.html</loc></url>
 <url><loc>https://gilberthan1011.github.io/linkSet/reference/pairdist-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/plot_genomic_ranges-linkSet-method.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/readvalidPairs.html</loc></url>
+<url><loc>https://gilberthan1011.github.io/linkSet/reference/reduceRegions-linkSet-method.html</loc></url>
 </urlset>
 
diff --git a/vignettes/hic_workthrough.Rmd b/vignettes/hic_workthrough.Rmd
@@ -30,6 +30,11 @@ We highly recommend you to use custom data instead of the example data provided
 
 
 ```{r setup}
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+if (!require(c("TxDb.Mmusculus.UCSC.mm10.knownGene","org.Mm.eg.db"), quietly = TRUE))
+    BiocManager::install(c("TxDb.Mmusculus.UCSC.mm10.knownGene","org.Mm.eg.db"))
 suppressPackageStartupMessages({
   library(linkSet)
   library(TxDb.Mmusculus.UCSC.mm10.knownGene)