This repository has been created to include the original code developed by Alicia Aranda Fernandez in the completion of Bioinformatics and Biostatistics master's thesis, resulting in QApckg R package.
As with any other package, the R folder includes the original code for each of the defined functions, while the man folder (generated automatically) incorporates all their documentation. The DESCRIPTION (package metadata) and NAMESPACE (list of created functions and dependencies) required files are also presented.
In addition, the repository includes the QApckg_0.1.0.pdf document corresponding to the package reference manual, and the compressed QApckg_0.1.0.tar.gz file which allows the local installation of the package.
It is important to note that all the presented code is derived from a subset of the scripts included in the following repository: https://github.com/aliafdz/QA_genotipat_pipeline
This package provides a set of functions for NGS data processing, quality analysis, filtering and demultiplexing. These functions are designed to be applied in consecutive order on Miseq raw data to obtain a set of intersected haplotypes for each evaluated sample. With this consensus haplotypes different kinds of computations can be made, i.e genotyping, variant calling and quasispecies diversity.
QApckg is not available in public repositories. To install this package, download
the QApckg_0.1.0.tar.gz file and execute this code:
install.packages("./QApckg_0.1.0.tar.gz", repos = NULL, type = "source")