Merge branch 'papercuts' into dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DIscBIO
 Date: 2021-04-28
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.2.0.9004
+Version: 1.2.0.9005
 Authors@R:
   c(
     person(

NEWS.md

@@ -1,33 +1,35 @@
 # DIscBIO (development version)
 
-This file documents the changes between stable releases of DIscBIO.
+* Fixed integration and unit tests (issue #22, #37)
+* Improved coding style (issue #38)
+* Removed dependency on `boot` (issue 26)
 
-# Version 1.2.0
+# DIscBIO 1.2.0
 
-- Added support for retrying to retrieve URLs (issue #29)
-- Removed use of duplicated (legacy) function _on unit tests only_
-- Improved detection of duplicated data on `NetAnalysis()`
-- Improved I/O behavior
-- Improved validation
-- Bug fixes
+* Added support for retrying to retrieve URLs (issue #29)
+* Removed use of duplicated (legacy) function _on unit tests only_
+* Improved detection of duplicated data on `NetAnalysis()`
+* Improved I/O behavior
+* Improved validation
+* Bug fixes
 
-# Version 1.1.0
+# DIscBIO 1.1.0
 
-- Added support for more gene types
-- Improved I/O behavior
-- Updated Binder notebooks
+* Added support for more gene types
+* Improved I/O behavior
+* Updated Binder notebooks
 
-# Version 1.0.1
+# DIscBIO 1.0.1
 
-- Bug fixes
-- Updated Binder notebook
+* Bug fixes
+* Updated Binder notebook
 
-# Version 1.0.0
+# DIscBIO 1.0.0
 
 Contains several changes from the [original work](https://github.com/SystemsBiologist/PSCAN), the most relevant of which are listed below:
 
-- Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests)
-- Functions have been isolated into their own R files
-- Function and package documentation were added
-- Test datasets were compressed to occupy less disk space
-- Bugs have been fixed
+* Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests)
+* Functions have been isolated into their own R files
+* Function and package documentation were added
+* Test datasets were compressed to occupy less disk space
+* Bugs have been fixed

R/internal-functions-samr-adapted.R

@@ -60,7 +60,7 @@ samr.const.patterndiscovery.response <- "Pattern discovery"
 #' Only used for array data.
 #' @param return.x Should the matrix of feature values be returned? Only useful
 #' for time course data, where x contains summaries of the features over time.
-#' Otherwise x is the same as the input data data\$x
+#' Otherwise x is the same as the input data
 #' @param knn.neighbors Number of nearest neighbors to use for imputation of
 #' missing features values. Only used for array data.
 #' @param random.seed Optional initial seed for random number generator