Merge pull request #21 from uclahs-cds/cran-fixes

CRAN fixes

Author: dan-knight

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bedr
 Type: Package
 Title: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
-Version: 1.1.2
+Version: 1.1.3
 Date: 2025-04-01
 Authors@R: c(
   person("Syed", "Haider", role = "aut"),
@@ -26,7 +26,7 @@ Suggests:
     rmarkdown (>= 0.9.5)
 VignetteBuilder: knitr
 License: GPL-2
-URL: https://github.com/uclahs-cds/public-R-bedr
-BugReports: https://github.com/uclahs-cds/public-R-bedr/issues
+URL: https://github.com/uclahs-cds/pacakage-bedr
+BugReports: https://github.com/uclahs-cds/package-bedr/issues
 Imports: testthat (>= 3.0.0), VennDiagram (>= 1.6.4), data.table (>= 1.8.11), R.utils (>= 2.0.2), yaml (>= 2.1.10), parallel, grid
 Config/testthat/edition: 3

NEWS.md

@@ -1,10 +1,8 @@
-# bedr 1.1.2 (2025-04-01)
+# bedr 1.1.3 (2025-04-01)
 
 
 ## Added
 
-- Add LICENSE.md to repository
-- Update DESCRIPTION to include URL and BugReports links
 - Add `method` argument to `in.region` function
 
 ## Changed
@@ -15,6 +13,17 @@
 ## Fixed
 
 - Replace outdated `autostart` in `fread` with `skip`.
+- Fix cross-reference format in manual
+- Update GitHub links
+
+
+# bedr 1.1.2 (2024-01-24)
+
+
+## Added
+
+- Add LICENSE.md to repository
+- Update DESCRIPTION to include URL and BugReports links
 
 
 # bedr 1.1.1 (2023-08-24)

man/bedr.plot.region.Rd

@@ -38,7 +38,7 @@ Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
 A grouping parameter for barplots.  Possible values include "input", "chr", or a categorical vector of length equal to the sum of the input.
 }
   \item{params}{
-Additional parameters for plotting or intersecting.  See \code{\link{venn.diagram}} function for possible options.
+Additional parameters for plotting or intersecting.  See \code{\link[VennDiagram]{venn.diagram}} function for possible options.
 }
   \item{verbose}{
 Include text messages.

man/in.region.Rd

@@ -13,6 +13,7 @@ in.region(
 	x,
 	y,
 	proportion.overlap = 1e-09,
+	method = "natural",
 	reciprocal.overlap = FALSE,
 	check.zero.based = TRUE,
 	check.chr = TRUE,
@@ -27,6 +28,7 @@ in.region(
   \item{x}{first region index in the form chr:start-stop.  regions in this index will be checked for intersection in the values of the second index.}
   \item{y}{second region index.}
   \item{proportion.overlap}{Defaults 1e-9 which is 1 bp.  See details below for the different interpretation between 0 and 1 based overlap}
+  \item{method}{Sorting method ("natural" by default)}
   \item{reciprocal.overlap}{Should the proportion.overlap be reciprocal}
   \item{check.zero.based}{should 0 based coordinates be checked}
   \item{check.chr}{should chr prefix be checked}