Merge pull request #108 from uclahs-cds/helenzhu-refactor_histogram_and_gh_functions

Refactor: Enforcing bin_width and addition of introns to GenomicHistogram

Author: helen-zhu

NAMESPACE

@@ -30,6 +30,7 @@ export(GenomicHistogram)
 export(Histogram)
 export(bigWig_to_histogram)
 export(bin_log_likelihood)
+export(coverage_to_histogram)
 export(create_coverageplot)
 export(create_histogram)
 export(create_layerplot)

NEWS.md

@@ -0,0 +1,52 @@
+
+# Change Log
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+## [Unreleased]
+
+### Added
+
+### Changed
+- S3 methods to allow numeric/Histogram/GenomicHistogram input in key segment_and_fit functions
+
+### Fixed
+
+## [1.3.0] - 2023-04-14
+
+### Added
+- Added summary statistics (mean, sd, var, skew) estimation from histogram objects [Pull #113](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/113)
+
+### Changed
+- Enforcing bin width and addition of intron-traversing bins in GenomicHistogram [Pull #108](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/108)
+
+## [1.2.0] - 2023-04-12
+
+### Added
+- Added a classic histogram plotting function [Pull #111](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/111)
+
+## [1.1.0] - 2023-03-09
+
+### Added
+- Maxiumum likelihood estimation for distribution parameters [Pull #97](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/97)
+- A vignette! [Pull #81](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/81)
+- Added `gamma_flip` as an available distribution [Pull #62](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/62)
+
+### Changed
+- New rules for `Histogram` and `GenomicHistogram` [Pull #76](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/76)
+  - `Histogram` uses a strictly continuous Base 0 system while `GenomicHistogram` uses a potentially disjoint Base 1 system
+  - Both are restricted to having a fixed `bin_width` in (n-1) bins
+- Add pkgdown build on new release [Pull #56](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/56)
+- Updated `find_consensus_model` to include user-specified weights and metric prioritization & addition of new RRA method [Pull #53](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/53)
+
+### Fixed
+- Bug in `segment_and_fit` - finer segmentation is required to initialize `meaningful_gaps_local` [Pull #73](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/73)
+- Refactored `create_trackplot` to use `BoutrosLab.plotting.general::create.scatterplot` as a base function thus increasing efficiency [Pull #71](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/71)
+- Refactored `find_uniform_segment` to reduce code redundancy [Pull #59](https://github.com/uclahs-cds/public-R-HistogramZoo/pull/59)
+
+## [1.0.0] - 2022-08-22
+
+### Added
+- First release!

R/GRanges-utils.R

@@ -1,5 +1,5 @@
 #' Converts a GRanges object from base 0 to base 1
-#' 
+#'
 #' @param gr a GRanges object in base 0
 #' @return a GRanges object in base 1
 base0_to_base1 <- function(gr){