Hello all, I have generated a nucleotide diversity plot based on the example in this protocol: https://cran.r-project.org/web/packages/PopGenome/vignettes/Whole_genome_analyses_using_VCF_files.pdf (pg. 15-17). Initially, I attempted to generate the plot using the following command:
slide <- sliding.window.transform(GENOME.class,10000,10000, type=2)
However, this method did not suit my VCF file well. It would return a length of 1000 with values reaching 0 for more than half of the vectors.
I decided to return to the protocol and use the default values in the PopGenome manual, with my new command as such:
TBGENOMEdefault.slide <- sliding.window.transform(TBGENOMEdefault.class,7,5, type=1)
When I use the sliding window analysis as type = 1, i.e SNPs, PopGenome is able to fully analyze, when I set the type = 2, i.e genetic regions, PopGenome fails to fully load the analysis.
My question is how do I interpret my plot? Is the data analyzed in 7bp windows? Since I set the value to 7 instead of 10000? How should I interpret the graph if its type = 1 (i.e SNP) instead of type = 2 (i.e Genetic regions)?
Any experts in PopGenome or anyone who has used this protocol before please help. As I am pleased with the graph but am not sure how to interpret the x-axis.
My plot and my code can be found here as I also posted the question on research gate https://www.researchgate.net/post/PopGenome_nucleotide_diversity_plot_interpretation
Thank you, Natalia G
https://docserv.uni-duesseldorf.de/servlets/DerivateServlet/Derivate-35086/Dissertation_Bastian_Pfeifer.pdf
Dr. Pfeifer's dissertation on the program for those who seek clarification.