Merge branch 'main' of github.com:uclahs-cds/public-R-NanoStringNorm …

…into danknight-copyright
uclahs-cds · Jan 18, 2025 · df55c15 · df55c15
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,11 +2,7 @@ Package: NanoStringNorm
 Type: Package
 Title: Normalize NanoString miRNA and mRNA Data
 Version: 3.0.0
-<<<<<<< HEAD
 Date: 2025-01-16
-=======
-Date: 2025-01-15
->>>>>>> 0ef4621656f9437cbea69a61fe742408648da16b
 Authors@R: c(
 	person(c("Daryl", "M."), "Waggott", role = "aut"),
 	person("Paul", "Boutros", email = "[email protected]", role = "cre"),

diff --git a/NEWS → NEWS.md b/NEWS → NEWS.md
@@ -1,103 +1,98 @@
-NanoStringNorm 3.0.0 2025-01-16
-----------------------------------------------------------------
+# NanoStringNorm 3.0.0 (2025-01-15)
 
-CHANGED
-* Updated copyright header comments to include UCLA.
+## Removed
+* Removed Excel `.xls` support due to broken CRAN dependency
 
-REMOVED
-* Removed Excel .xls support due to broken CRAN dependency
-
-ADDED
+## Added
 * Added CSV support for nCounter Excel files. Excel files must be converted externally.
 
+## Changed
+* Update changelog to Markdown format
+
 
-NanoStringNorm 2.0.0 2023-03-21
-----------------------------------------------------------------
+# NanoStringNorm 2.0.0 (2023-03-21)
 
-REMOVED
+## Removed
 * Removed vsn functionality due to broken CRAN dependency
 
-NanoStringNorm 1.2.1 2017-12-11
-----------------------------------------------------------------
 
-BUG
+# NanoStringNorm 1.2.1 (2017-12-11)
+
+## Fixed
 * Fixed unclosed file connection bug
 
-NanoStringNorm 1.2.0 2017-08-18
-----------------------------------------------------------------
 
+# NanoStringNorm 1.2.0 (2017-08-18)
+
+## Fixed
 * fixed read.markup.RCC() error on new NanoString nCounter FLEX instrument
 
-NanoStringNorm 1.1.22 2017-06-30
-----------------------------------------------------------------
 
+# NanoStringNorm 1.1.22 (2017-06-30)
+
+## Added
 * NanoStringNorm
  - added parameters "CodeCount.summary.target" and "SampleContent.summary.target"
  - these parameters allow users to specify expected positive control and housekeeping probe summary values, which are used during the cross-sample normalization
  - this update allows for sample-independent normalization of various CodeCount and SampleContent methods 
 
-NanoStringNorm 1.1.17 2014-01-15
-----------------------------------------------------------------
 
+# NanoStringNorm 1.1.17 (2014-01-15)
+
+## Fixed
 * fixed error using only one control gene.  the matrix in the apply statement was getting changed to vector.
 
-NanoStringNorm v1.1.16 2013-09-01
-----------------------------------------------------------------
 
+# NanoStringNorm v1.1.16 (2013-09-01)
+
+## Changed
 * lme4
- -lme4 doesn't work on some platforms
- -NSN "suggests" lme4 but errored out if it was missing due to examples
- -solution was add if(require(pkg)) in examples
- -this was done for all suggests packages
-
+  * lme4 doesn't work on some platforms
+  * NSN "suggests" lme4 but errored out if it was missing due to examples
+  * solution was add if(require(pkg)) in examples
+  * this was done for all suggests packages
 * Runit
-  if(require(RUnit)) was added to NanoStringNorm.unitTests.R.  Runit was recommended by BR to be a suggests and not a depends.  
- - package needs to be able to run/test with and without suggest packages
-
+  * if(require(RUnit)) was added to NanoStringNorm.unitTests.R.  Runit was recommended by BR to be a suggests and not a depends.  
+  * package needs to be able to run/test with and without suggest packages
+
+## Fixed 
 * Rd line length.  R-devel fails on example/usage length of 90.
-
 * ::: dropped in code due to check warning
 
 
-NanoStringNorm 1.1.15 2014-01-15
-----------------------------------------------------------------
+# NanoStringNorm 1.1.15 (2014-01-15)
 
+## Fixed
 * R check compatablility
- - reduced size of high resolution bitmaps used in vignette (100kb saved!)
- - changed Nanostring to NanoString in text (seriously!)
- - made googleVis example conditional depending on installation.  the package is under "suggests"
+* reduced size of high resolution bitmaps used in vignette (100kb saved!)
+* changed Nanostring to NanoString in text (seriously!)
+* made googleVis example conditional depending on installation.  the package is under "suggests"
 * bug when negative control removes signal from all samples
 
 
-NanoStringNorm 1.1.14 2013-04-04
-----------------------------------------------------------------
-
-BUG FIXES
+# NanoStringNorm 1.1.14 (2013-04-04)
 
+## Fixed
 * sample.content.norm.  added some error handling for cases where rna.content was estimated to be zero, resulting in normalization factors that were infinity and errors in norm.comp
 
-NanoStringNorm 1.1.12 2012-12-01
-----------------------------------------------------------------
 
-BUG FIXES
+# NanoStringNorm 1.1.12 (2012-12-01)
 
+## Fixed
 * read.xls.RCC.  more informative error messages and allowed id instead of sample.id in header
 * Plot.NanoStringNorm.gvis.  set default browser if not set.
 
-NanoStringNorm 1.1.11 2012-10-01
-----------------------------------------------------------------
-
-MINOR FEATURES
+# NanoStringNorm 1.1.11 (2012-10-01)
 
+## Added
 * added parameter "guess.cartridges" in NanoStringNorm function.  Cartridge estimates can be estimated from sample order and used in batch effect estimates
 * in Plot.NanoStringNorm the control types have different symbols
 * added some text to better describe the figures.  also replaced the png with pdf for better resolution
 * made it so you can add manual and auto labels at the same time
 * added options label.n to specify the number of outliers to plot and label.as.legend to allow the labels to be written as a legend to avoid messy overlaps
 * output FDR qvalues
 
-BUG FIXES
-
+## Fixed
 * Plot.NanoStringNorm had a missing curly brace and forgotten browser statement
 * Shifted labels on positive.control plot to avoid overlap if long
 * Added regex for positive control names in cv plot, probe.correction function and norm.comp.  sometimes the positive controls are named differently causing them to be missed during calculations
@@ -106,11 +101,10 @@ BUG FIXES
 * Fixed norm.factor plot positions when only one plot
 * changed low.cv.geo.mean method to better find low cv genes 
 
-NanoStringNorm 1.1.10 2012-09-01
-----------------------------------------------------------------
 
-MINOR FEATURES
+# NanoStringNorm 1.1.10 (2012-09-01)
 
+## Added
 * Added colour argument `col` in Plot.NanoStringNorm to change default plotting colours
 * Added function read.markup.RCC to process single sample markup RCC files
 * Changed NanoStringNorm log argument to `take.log`
@@ -121,9 +115,7 @@ MINOR FEATURES
 * Added argument `icc.method` in norm.comp to choose between anova (fast) and mixed (more appropriate)
 * Changed default sample name in read.xls.rcc to file.name
 
-
-BUG FIXES
-
+## Fixed
 * Added check in NanoStringNorm to check if input is a matrix, list, or data.frame
 * Added check for `Code.Class` colum in norm.comp.  The col is referenced but the data is not exhaustively checked.  The check was also added to the read.markup.RCC function
 * Added check for problem input in read.xls.RCC