The operation between the results of fixationSites
and parallelSites
.
paraFixSites(x, ...)
# S3 method for phylo
paraFixSites(
x,
alignment = NULL,
seqType = c("AA", "DNA", "RNA"),
Nmin = NULL,
reference = NULL,
gapChar = "-",
minSkipSize = NULL,
...
)
# S3 method for treedata
paraFixSites(x, ...)
# S3 method for lineagePath
paraFixSites(
x,
minEffectiveSize = NULL,
searchDepth = 1,
method = c("compare", "insert", "delete"),
...
)
# S3 method for sitesMinEntropy
paraFixSites(
x,
category = c("intersect", "union", "parallelOnly", "fixationOnly"),
minSNP = NULL,
mutMode = c("all", "exact", "pre", "post"),
...
)
A lineagePath
object returned from lineagePath
function.
further arguments passed to or from other methods.
An alignment
object. This commonly can be from
sequence parsing function in the seqinr
package. Sequence
names in the alignment should include all tip.label
in the tree
The type of the sequence in the alignment file. The default is "AA" for amino acid. The other options are "DNA" and "RNA".
The parameter for identifying phylogenetic pathway using SNP. If
provided as fraction between 0 and 1, then the minimum number of SNP will
be total tips times Nmin
. If provided as integer greater than 1, the
minimum number will be Nmin
.
Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering
The character to indicate gap. The numbering will skip the
gapChar
for the reference sequence.
The minimum number of tips to have gap or ambiguous amino acid/nucleotide for a site to be ignored in other analysis. This will not affect the numbering. The default is 0.8.
The minimum number of tips in a group.
The function uses heuristic search but the termination of
the search cannot be intrinsically decided. searchDepth
is needed to
tell the search when to stop.
The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.
Could be parallelOnly
, fixationOnly
,
intersect
or union
.
The minimum number of mutations to be qualified as parallel on at least two lineages. The default is 1.
The strategy for finding parallel site. The default all
is to consider any mutation regardless of the amino acid/nucleotide before
and after mutation; Or exact
to force mutation to be the same; Or
pre
/post
to select the site having amino acid/nucleotide
before/after mutation.
A paraFixSites
object.