This code facilitates identification of ospC genotypes from terminal restriction fragment length polymorphism analysis of B. burgdorferi samples (Tsao et al 2013). You’ll need R andPeakScanner (version 1.0).
After fragment analysis in PeakScanner, copy the generated data table for all samples into a text file (more detailed instructions in main code comments). The code steps through each sample in this file individually, identifying the best matches to known ospC genotypes based on the data peaks.
R code and associated files:
You can figure out how to format your data according to the manuscript and sample file, or you can use these templates. It’s probably about the same amount of effort either way.
PeakScanner setting files (put these in the specified folders within the PeakScanner program folder, and select them within PeakScanner to analyze samples):
- ospC_Analysis Method.met (put in Analysis Methods folder)
- ospC_SampleTable.xml (put in Sample Table Settings folder)
- ospC_SizingTable.xml (put in Sizing Table Settings folder)
- ospC_SizeStd-ROX500.sts (put in Size Standards folder)