buildPratchet - Wrapper for phangorn::pratchet
Description¶
Wrapper for phangorn::pratchet
Usage¶
buildPratchet(
clone,
seq = "sequence",
asr = "seq",
asr_thresh = 0.05,
tree = NULL,
asr_type = "MPR",
verbose = 0,
resolve_random = TRUE,
data_type = "DNA"
)
Arguments¶
- clone
airrCloneobject- seq
- sequece column in
airrCloneobject - asr
- return sequence or probability matrix?
- asr_thresh
- threshold for including a nucleotide as an alternative
- tree
- fixed tree topology if desired.
- asr_type
- MPR or ACCTRAN
- verbose
- amount of rubbish to print
- resolve_random
- randomly resolve polytomies?
- data_type
- Are sequences DNA or AA?
Value¶
phylo object created by phangorn::pratchet with nodes
attribute containing reconstructed sequences.