Dev

.Rhistory

@@ -0,0 +1,103 @@
+pkgdown::build_site()
+# Build the package
+{
+options(pkgdown.internet = FALSE)
+Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+gwtwd()
+getwd()
+install.packages("devtools")
+# Build the package
+{
+options(pkgdown.internet = FALSE)
+Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+# Build the package
+{
+options(pkgdown.internet = FALSE)
+Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+# Build the package
+{
+options(pkgdown.internet = FALSE)
+Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+install.packages(c("snpStats", "reshape2"))
+# Build the package
+{
+options(pkgdown.internet = FALSE)
+Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+getwd()
+install.packages("devtools")
+install.packages(c("snpStats", "reshape2"))
+install.packages(c("reshape2"))
+if (!require("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+BiocManager::install("snpStats")
+# Build the package
+{
+# options(pkgdown.internet = FALSE)
+# Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+.Last.error
+devtools::document()
+# Build the package
+{
+# options(pkgdown.internet = FALSE)
+# Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+devtools::document()
+# Build the package
+{
+# options(pkgdown.internet = FALSE)
+# Sys.setenv("PKGDOWN_INTERNET" = "false")
+# setwd("/home/vinicius/projects/brangus/SNPtools")
+devtools::document()
+devtools::clean_dll()
+devtools::install(upgrade = "never")
+pkgdown::build_site()
+}
+# Install devtools if not already installed
+install.packages("devtools")
+# Install SNPtools from GitHub
+devtools::install_github("viniciusjunqueira/SNPtools")
+usethis::edit_r_environ()
+# Install SNPtools from GitHub
+devtools::install_github("viniciusjunqueira/SNPtools")
+library(SNPtools)

DESCRIPTION

@@ -6,6 +6,7 @@ Authors@R: c(
            email = "junqueiravinicius@hotmail.com", role = c("aut", "cre")))
 Maintainer: Vinícius Junqueira <junqueiravinicius@hotmail.com>
 Description: SNPtools provides an integrated suite of tools for handling SNP genotype data in large-scale genetic studies. The package supports importing and merging genotype files, performing quality control on SNP markers and samples, and preparing data for downstream analyses using popular software such as FImpute and PLINK. It offers S4 classes and methods to efficiently encapsulate SNP data, along with utilities for generating genotype summary statistics and visualization. Additional functionalities in the current version include anticlustering approaches for batch effect control, automated script generation for external software, and streamlined workflows for large datasets commonly encountered in animal and plant breeding programs. The package is designed to facilitate reproducible and scalable SNP data analyses in quantitative and statistical genetics.
+Logo: man/figures/logo.png
 Depends:
     R (>= 4.1.0),
     snpStats,
@@ -23,7 +24,7 @@ Suggests:
     rmarkdown
 VignetteBuilder: knitr
 Encoding: UTF-8
-# License: GPL-3
+License: GPL-3
 URL: https://viniciusjunqueira.github.io/SNPtools
 BugReports: https://github.com/viniciusjunqueira/SNPtools/issues
 RoxygenNote: 7.3.2

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="inst/figures/logo.png" alt="SNPtools logo" width="200"/>
+  <img src="man/figures/logo.png" alt="SNPtools logo" width="200"/>
 </p>
 
 # SNPtools
@@ -23,23 +23,22 @@ devtools::install_github("viniciusjunqueira/SNPtools")
 ```
 ---
 
-## Usage
+## 📖 Documentation
 
-```r
-library(SNPtools)
+The full package website with detailed function reference and vignettes is available at:
+
+- [SNPtools pkgdown site](https://viniciusjunqueira.github.io/SNPtools/)
+
+Key pages:
 
-# Example: print a formatted header
-qc_header("Starting genotype preprocessing")
+- [Reference index](https://viniciusjunqueira.github.io/SNPtools/reference/index.html) 
+- [Vignettes and Tutorials](https://viniciusjunqueira.github.io/SNPtools/articles/)
+
+---
 
-# Example configuration list
-configs <- list(
-  list(path = "panel1", fields = list(sample = 2, snp = 1, allele1 = 7, allele2 = 8, confidence = 9)),
-  list(path = "panel2", fields = list(sample = 2, snp = 1, allele1 = 7, allele2 = 8, confidence = 9), threshold = 0.10)
-)
+## 📄 License
 
-# Import and combine genotype data
-combined_data <- import_geno_list(configs)
+SNPtools is licensed under the GPL-3 license. See the [LICENSE](LICENSE) file for details.
 
-# Print a summary
-summary(combined_data)
-```
+[![pkgdown](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://viniciusjunqueira.github.io/SNPtools/)
+[![GitHub issues](https://img.shields.io/github/issues/viniciusjunqueira/SNPtools)](https://github.com/viniciusjunqueira/SNPtools/issues)