Workflow
Work begins with a variant call format file (VCF). A reference file (FASTA) and an annotation file are also suggested. These later two files are not necessary, but I feel they contribute substantially. The below flowchart outlines the major steps involved with vcfR use.
The green rectangles contain functions that the user will want to become familiar with. There are effectively three phases in the workflow: reading in data, processing the objects in memory and plotting the data graphically. Reading in the data frequently presents a bottleneck. Unfortunately, this is typically due to the time it takes to read from a drive and therefore may not be anything I can improve on. Once the data are in memory we can manipulate it. VcfR uses Rcpp to implement functions written in C++ to try to improve the performance of these functions. Lastly, we visualize the objects. Visualization relies on R’s base graphics package. This is also something that I am not likely to be able to improve on if it becomes a bottleneck. By dividing the analysis into these three phases I’ve divided that workflow into things I may be able to improve upon through my code writing, and things which I have little control over.