updated vignette and readme

DESCRIPTION

 Package: sigident
 Title: Signature Analyses in Genomic Expression Sets
-Version: 0.0.4.9002
+Version: 0.0.5
 Authors@R: 
     c(person(given = "Lorenz A.",
              family = "Kapsner",
@@ -23,7 +23,7 @@ URL: https://gitlab.miracum.org/clearly/sigident
 BugReports: https://gitlab.miracum.org/clearly/sigident/issues
 Encoding: UTF-8
 VignetteBuilder: knitr
-Date: 2020-04-07
+Date: 2020-04-21
 biocViews: 
 Imports: 
     data.table,
@@ -46,6 +46,7 @@ Suggests:
     rmarkdown,
     qpdf,
     lintr
-Remotes:  
-    url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/development/sigident.preproc-development.zip,
-    url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/development/sigident.func-development.zip
+Remotes: 
+    url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/v0.0.4/sigident.preproc-v0.0.4.zip,
+    url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/v0.0.3/sigident.func-v0.0.3.zip
+RoxygenNote: 7.1.0

Readme.md

-# sigident (!!! currently under development !!!)
+# sigident (!!! under development !!!)
 
 <!-- badges: start -->
 [![pipeline status](https://gitlab.miracum.org/clearly/sigident/badges/master/pipeline.svg)](https://gitlab.miracum.org/clearly/sigident/commits/master)
@@ -21,7 +21,7 @@ Currently implemented features are:
 
 You can install *sigident* with the following commands in R:
 
-``` r
+```r
 options('repos' = 'https://ftp.fau.de/cran/')
 install.packages("devtools")
 devtools::install_git("https://gitlab.miracum.org/clearly/sigident.git")
@@ -29,9 +29,7 @@ devtools::install_git("https://gitlab.miracum.org/clearly/sigident.git")
 
 The version of the package, which was used for the publication [A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning](https://www.mdpi.com/2072-6694/11/10/1606) can anytime be reproduced using the version tag *v0.0.2* during the installation process:
 
-``` r
-options('repos' = 'https://ftp.fau.de/cran/')
-install.packages("devtools")
+```r
 devtools::install_git("https://gitlab.miracum.org/clearly/sigident.git", ref = "v0.0.2")
 ```
 

data-raw/devstuffs.R

@@ -19,7 +19,7 @@ my_desc$del("Maintainer")
 # Vignette Builder
 my_desc$set("VignetteBuilder" = "knitr")
 # Set the version
-my_desc$set_version("0.0.4.9002")
+my_desc$set_version("0.0.5")
 # The title of your package
 my_desc$set(Title = "Signature Analyses in Genomic Expression Sets")
 # The description of your package
@@ -85,17 +85,18 @@ usethis::use_package("knitr", type = "Suggests")
 usethis::use_package("lintr", type = "Suggests")
 
 # Development package
-mytag <- "development"
-devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.preproc", ref = mytag, upgrade = "always")
-mytag2 <- "development"
-devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.func", ref = mytag2, upgrade = "always")
+preproc_tag <- "v0.0.4"
+func_tag <- "v0.0.3"
+
+devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.preproc", ref = preproc_tag, upgrade = "always")
+devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.func", ref = func_tag, upgrade = "always")
 # https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html
 desc::desc_set_remotes(c(
   paste0(
-    "url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/", mytag, "/sigident.preproc-", mytag, ".zip"),
+    "url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/", preproc_tag, "/sigident.preproc-", preproc_tag, ".zip"),
   # sigident.func is only required for the vignettes (therefore a "suggests"-package)
   paste0(
-    "url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/", mytag2, "/sigident.func-", mytag2, ".zip")
+    "url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/", func_tag, "/sigident.func-", func_tag, ".zip")
 ),
 file = usethis::proj_get())
 

vignettes/.gitignore

-*.html
-*.R
-sigident-Howto_Microarray-Dateien/
-inst/application/data
-data
-vignettes/geodata
-vignettes/plots
-vignettes/csv
-vignettes/GSE19188
-vignettes/preview.dir
-!/.gitlab-ci.yml
-geodata
-csv
-plots
-*.Rproj
-.Rproj*
-.Rhistory
-.RData
-tests/testthat/testdata
-tests/testthat/plots
-*.rds
-metadatadir
-metadata
-vignettes/metadata
-vignettes/*.csv
-vignettes/figure
-vignettes/tables
-tables
-vignettes/.build.timestamp
+/*/
+/*
+!/*.html
+!/*.Rmd

vignettes/sigident-Howto_Microarray.Rmd

@@ -16,6 +16,11 @@ knitr::opts_chunk$set(
 )
 ```
 
+The R package `sigident` is the core package of the `sigident` package framework. This framework consists of several packages which can be used to perform analyses of gene signatures. The following packages are included in the framework: 
+* Core package: [sigident](https://gitlab.miracum.org/clearly/sigident) 
+* Data preprocessing: [sigident.preproc](https://gitlab.miracum.org/clearly/sigident.preproc) 
+* Functional analyses: [sigident.func](https://gitlab.miracum.org/clearly/sigident.func)  
+
 # Prerequisites and installation 
 
 ## Install sigident.preproc package
@@ -44,7 +49,7 @@ devtools::install_git("https://gitlab.miracum.org/clearly/sigident.git")
 
 In order to use this R package and its functions, you need to prepare a merged gene expression dataset. The workflow to achieve this is presented in the following by making use of the R package `sigident.preproc`.
 
-For a detailed background and description of the following steps please view the `sigident.preproc` package's vignette.
+For a more detailed background and description of the following steps please view the `sigident.preproc` package's [vignette](https://gitlab.miracum.org/clearly/sigident_vignettes).
 
 ## Initialization of important variables
 
@@ -126,7 +131,7 @@ Before using the `sigident` package, these variables need to be defined properly
 
 In order to use this R package and its functions, you need to prepare a merged gene expression dataset. The workflow to achieve this is presented in the following by making use of the R package `sigident.preproc`.
 
-For a detailed background on the following steps please view the `sigident.preproc` package's vignette.
+For a detailed background on the following steps please view the `sigident.preproc` package's [vignette](https://gitlab.miracum.org/clearly/sigident_vignettes).
 
 ```{r}
 # general
@@ -206,7 +211,7 @@ gc()
 
 ## Gene enrichment
 
-For a detailed background and description of the following steps please view the `sigident.func` package's vignette.
+For a detailed background and description of the following steps please view the `sigident.func` package's [vignette](https://gitlab.miracum.org/clearly/sigident_vignettes).
 
 ```{r}
 deg_entrez <- unique(mergedset@featureData@data$ENTREZ_GENE_ID)
@@ -527,7 +532,7 @@ knitr::kable(
 
 ### Model performance measurements
 
-Additionally, the confusion matrix and the calculated performance metrices can be printed out for each model. 
+Additionally, the confusion matrix and the calculated performance metrics can be printed out for each model. 
 
 #### Lasso (min)