dumpVariants: Print sequence to file
Description
A function to output all sequences or just unique
sequences to a fasta file
Usage
dumpVariants(mlgtResultObject, markers = names(mlgtResultObject@markers), samples = mlgtResultObject@samples, fileSuffix = "variantDump.fasta", uniqueOnly = FALSE)
Arguments
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.
Details
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.