Description Usage Arguments Details Value Note References
View source: R/coil_functions.R
Extract barcode for use in COIL program
1 | extractBarcode(gdsfile, variant.id, barcode.file)
|
gdsfile |
a |
variant.id |
a numeric vector of variant identifiers |
barcode.file |
character name of output file |
Generate SNP barcode using supplied variant ids. This is constructed by collapsing alleles over the variant ids, forming a barcode for each sample. Then a barcode file containing sample ids + barcode is generated and can be supplied to the COIL web-app or to the command line COIL program.
data.frame containing barcode for each sample
Need to look at how COIL constructed it's orginal barcode. Esp. het calls.
Galinsky, Kevin, et al. "COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data." Malaria journal 14.1 (2015): 4.
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