findSites {sitePath} | R Documentation |
Single nucleotide polymorphism (SNP) in the whole package refers to
variation of amino acid. findSNPsite
will try to find SNP in
the multiple sequence alignment. A reference sequence
and gap character may be specified to number the site. This is
irrelevant to the intended analysis but might be helpful to evaluate
the performance of fixationSites
.
After finding the lineagePath
of a phylogenetic tree,
fixationSites
uses the result to find those sites that show
fixation on some, if not all, of the lineages. Parallel evolution is
relatively common in RNA virus. There is chance that some site be fixed
in one lineage but does not show fixation because of different
sequence context.
After finding the lineagePath
of a phylogenetic tree,
multiFixationSites
uses random sampling on the original tree
and applies the method used in fixationSites
to each sampled
tree and summarize the results from all the samples.
SNPsites(tree, minSNP = NULL) ## S3 method for class 'lineagePath' fixationSites( paths, minEffectiveSize = NULL, searchDepth = 1, method = c("compare", "insert", "delete"), ... ) ## S3 method for class 'lineagePath' multiFixationSites( paths, samplingSize = NULL, samplingTimes = 100, minEffectiveSize = 0, searchDepth = 1, method = c("compare", "insert", "delete"), ... )
tree |
The return from |
minSNP |
Minimum number of amino acid variation to be a SNP |
paths |
a |
minEffectiveSize |
A vector of two integers to specifiy minimum tree tips involved before/after mutation. Otherwise the mutation will not be counted into the return. If more than one number is given, the ancestral takes the first and descendant takes the second as the minimum. If only given one number, it's the minimum for both ancestral and descendant. |
searchDepth |
The function uses heuristic search but the termination of the search
cannot be intrinsically decided. |
method |
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. |
... |
further arguments passed to or from other methods. |
samplingSize |
The number of tips sampled for each round of resampling. It shoud be at least 10th and at most nine 10ths of the tree tips. |
samplingTimes |
The total times of random sampling to do. It should be greater than 100. |
SNPsite
returns a list of qualified SNP site
fixationSites
returns a list of fixation mutations
with names of the tips involved.
multiFixationSites
returns sites with multiple fixations.
data(zikv_tree_reduced) data(zikv_align_reduced) tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced) SNPsites(tree) fixationSites(lineagePath(tree))