dumpVariants: Print sequence to file
In mlgt: Multi-Locus Geno-Typing

A function to output all sequences or just unique sequences to a fasta file

  dumpVariants(mlgtResultObject,
    markers = names(mlgtResultObject@markers),
    samples = mlgtResultObject@samples,
    fileSuffix = "variantDump.fasta", uniqueOnly = FALSE)

`mlgtResultObject`	an object of class `mlgtResult`
`markers`	Which markers to output
`samples`	Which samples to output
`fileSuffix`	Add a common suffix to the file names. Usefull for keeping track of different sets of sequences.
`uniqueOnly`	Only output single copy of each sequence. A count for each sequence are appended to the names.

The sequence variants stored within an object of class mlgtResult are not very easy to extract. This function will output all variants or all variant for specific markers and samples into fasta files. Users can select to only output unique sequences or the full alignment including duplicated sequences. One file will be created for each marker/sample pair.

mlgt documentation built on May 1, 2019, 8:45 p.m.