Commit 4a462ef0 authored by Lorenz Kapsner's avatar Lorenz Kapsner
Browse files

updated vignette and readme

parent 9185712f
Pipeline #8252 passed with stages
in 57 minutes and 22 seconds
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
# 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")
```
......
......@@ -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$set(Title = "Signature Analyses in Genomic Expression Sets")
# The description of your package
......@@ -85,17 +85,18 @@ usethis::use_package("knitr", type = "Suggests")
usethis::use_package("lintr", type = "Suggests")
# Development package
mytag <- "development"
devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.preproc", ref = mytag, upgrade = "always")
mytag2 <- "development"
devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.func", ref = mytag2, upgrade = "always")
preproc_tag <- "v0.0.4"
func_tag <- "v0.0.3"
devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.preproc", ref = preproc_tag, upgrade = "always")
devtools::install_git(url = "https://gitlab.miracum.org/clearly/sigident.func", ref = func_tag, upgrade = "always")
# https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html
desc::desc_set_remotes(c(
paste0(
"url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/", mytag, "/sigident.preproc-", mytag, ".zip"),
"url::https://gitlab.miracum.org/clearly/sigident.preproc/-/archive/", preproc_tag, "/sigident.preproc-", preproc_tag, ".zip"),
# sigident.func is only required for the vignettes (therefore a "suggests"-package)
paste0(
"url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/", mytag2, "/sigident.func-", mytag2, ".zip")
"url::https://gitlab.miracum.org/clearly/sigident.func/-/archive/", func_tag, "/sigident.func-", func_tag, ".zip")
),
file = usethis::proj_get())
......
*.html
*.R
sigident-Howto_Microarray-Dateien/
inst/application/data
data
vignettes/geodata
vignettes/plots
vignettes/csv
vignettes/GSE19188
vignettes/preview.dir
!/.gitlab-ci.yml
geodata
csv
plots
*.Rproj
.Rproj*
.Rhistory
.RData
tests/testthat/testdata
tests/testthat/plots
*.rds
metadatadir
metadata
vignettes/metadata
vignettes/*.csv
vignettes/figure
vignettes/tables
tables
vignettes/.build.timestamp
/*/
/*
!/*.html
!/*.Rmd
......@@ -16,6 +16,11 @@ knitr::opts_chunk$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)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment