diff --git a/DESCRIPTION b/DESCRIPTION index fbea664..a31883f 100644 --- a/DESCRIPTION +++ b/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( diff --git a/NEWS.md b/NEWS.md index 8494128..621f5fa 100644 --- a/NEWS.md +++ b/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 diff --git a/R/internal-functions-samr-adapted.R b/R/internal-functions-samr-adapted.R index f9a5f7e..f85e547 100644 --- a/R/internal-functions-samr-adapted.R +++ b/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 diff --git a/man/sammy.Rd b/man/sammy.Rd index 66a1f87..3a5442a 100644 --- a/man/sammy.Rd +++ b/man/sammy.Rd @@ -74,7 +74,7 @@ Only used for array data.} \item{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} \item{knn.neighbors}{Number of nearest neighbors to use for imputation of missing features values. Only used for array data.}