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package_dev.Rmd
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---
title: "package_dev"
---
```{r setup, include=FALSE}
library(devtools)
library(testthat)
```
To do:
correlation function (pval, pairwise.complete.obs)
```{r initial setup}
use_mit_license()
use_readme_rmd()
use_pipe()
```
```{r package startup}
load_all()
```
Dependencies
```{r}
use_package("ggplot2")
use_package("ggrepel")
use_package("rlang")
use_package("scales")
use_package("magrittr")
use_package("dplyr")
use_package("openxlsx")
use_package("ComplexHeatmap")
use_package("circlize")
use_package("ggdendro")
use_package("paletteer")
use_package("BiocParallel")
use_package("patchwork")
use_package("limma")
use_package("edgeR")
use_package("DESeq2")
use_package("GSVA")
use_package("fgsea")
use_package("tximport")
use_package("AnnotationDbi")
use_package("igraph")
use_package("msigdbr")
use_package("rtracklayer", type = "Suggests")
use_package("sparseMatrixStats", type = "Suggests")
use_package("tidygraph", type = "Suggests")
use_package("graphlayouts", type = "Suggests")
use_package("GSEABase", type = "Suggests")
use_package("IHW", type = "Suggests")
use_package("biomaRt", type = "Suggests")
use_package("clusterProfiler", type = "Suggests")
use_package("org.Hs.eg.db", type = "Suggests")
use_package("colorDF", type = "Suggests")
use_package("colourpicker", type = "Suggests")
use_package("prismatic", type = "Suggests")
use_package("dendsort", type = "Suggests")
use_package("crayon", type = "Suggests")
use_package("qualpalr", type = "Suggests")
use_package("survival", type = "Suggests")
use_package("survminer", type = "Suggests")
use_package("rms", type = "Suggests")
use_package("cowplot", type = "Suggests")
use_package("missMDA", type = "Suggests")
use_package("plyr", type = "Suggests")
use_package("tibble", type = "Suggests")
use_package("tidyr", type = "Suggests")
use_package("yaml", type = "Suggests")
```
Add R scripts
```{r}
use_r("meta_functions.R")
use_r("plotting_functions")
use_r("gene_functions.R")
use_r("imports.R")
```
Update documentation
```{r}
# Code > Insert Roxygen Skeleton
document()
# devtools::build_manual()
# roxygen2::roxygenize()
```
Add unit tests
```{r}
lapply(list.files("R/", pattern = ".R"), use_test)
```
Test/check
```{r check}
# test()
check() # or Build > Check Package
```
```{r}
usethis::use_build_ignore("package_dev.Rmd")
usethis::use_build_ignore("desktop.ini")
```
```{r}
devtools::build_readme()
```
Install the package
```{r}
install()
```