extractBarcode: Extract barcode for use in COIL program

In sa-lee/moimix: Estimating mulitplicity of infection from high-throughput sequencing data

Description

Extract barcode for use in COIL program

Usage

extractBarcode(gdsfile, variant.id, barcode.file)

Arguments

gdsfile	a SeqVarGDSClass object
variant.id	a numeric vector of variant identifiers
barcode.file	character name of output file

Details

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.

Value

data.frame containing barcode for each sample

Note

Need to look at how COIL constructed it's orginal barcode. Esp. het calls.

References

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.

sa-lee/moimix documentation built on April 23, 2020, 10:32 a.m.