refactor: remove HiContactsData dependency

js2264 · Sep 14, 2023 · 178eacf · 178eacf
1 parent ec5c3e2
commit 178eacf
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Showing 5 changed files with 3 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,7 +32,6 @@ Imports:
     methods, 
     utils
 Suggests: 
-    HiContactsData,
     rtracklayer,
     BiocStyle,
     covr,

diff --git a/R/ginteractions-construct.R b/R/ginteractions-construct.R
@@ -96,7 +96,7 @@
 #' # 4. GInteractions from a real like pairs files
 #' ####################################################################
 #' 
-#' pairsf <- HiContactsData::HiContactsData('yeast_wt', 'pairs.gz')
+#' pairsf <- system.file('extdata', 'pairs.gz', package = 'plyinteractions')
 #' pairs <- read.table(pairsf, comment.char = '#', header = FALSE)
 #' head(pairs)
 #' pairs |> 

diff --git a/inst/extdata/pairs.gz b/inst/extdata/pairs.gz
diff --git a/man/ginteractions-construct.Rd b/man/ginteractions-construct.Rd
diff --git a/vignettes/plyinteractions.Rmd b/vignettes/plyinteractions.Rmd
@@ -113,7 +113,7 @@ tabular data import functions (including `fread` or `vroom` for larger files),
 and readily coerced into `GInteractions` with `as_ginteractions`. 
 
 ```{r}
-pairs_file <- HiContactsData::HiContactsData('yeast_wt', 'pairs.gz')
+pairs_file <- system.file('extdata', 'pairs.gz', package = 'plyinteractions')
 pairs_df <- read.delim(pairs_file, sep = "\t", header = FALSE, comment.char = "#")
 head(pairs_df)
 pairs <- as_ginteractions(pairs_df,