gbedwell/rigrag: Identification of Recurrently Targeted Genes and Recurrently Avoided Genes During HIV-1 Infection

rigrag was written to aid in the characterization of recurrent integration genes (RIGs) and recurrent avoided genes (RAGs) during HIV-1 infection. This package is intended to be run following intersection of integration site coordinates with a relevant gene annotation file. Examples of these upstream steps can be found within the 'example_files/intersection_example.sh' file at https://github.com/gbedwell/random_integration. Note that the intersection scheme described above adds a column containing the total number of integration sites from the original integration site file. To run rigrag, the user needs to define a directory containing all of the integration site files to be analyzed. These files can be easily imported using built-in functions if their names share a common pattern (this is recommended). Following import, the user needs to define a list of sample identifiers for each integration site file. It is important that these identifiers are in the same order as the files in the file list. Spaces, pound signs, and plus signs are allowed in the sample identifiers. Any file names of files output with rigrag functions will be cleaned to remove these characters. rigrag contains functions to easily calculate all of the relevant model parameters and boundaries for every sample in the analysis. Models can be generated for either random fragmentation or for pattern fragmentation (i.e. restriction digestion). The specific enzyme cocktail must be specified. Additional pattern fragmentation models for different enzyme combinations will be added over time. In addition, rigrag automatically categorizes outlier types based on the sample-specific model parameters. rigrag functions have been written to conveniently output particular files and plots as desired to eliminate potentially troublesome plotting issues. For examples of rigrag plots, see Bedwell, et al. Phenomenological Modelling of Random Integration Identifies Genes Recurrently Targeted and Recurrently Avoided in Acute and Persistent HIV-1 Infection. JOURNAL HERE. 2020. Alternatively, example rigrag usage is provided in the 'gbedwell/random_integration/example_files' GitHub repository.

install.packages("remotes")
remotes::install_github("gbedwell/rigrag")