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 the result to find those sites that show
multiple fixations on some, if not all, of the lineages.
SNPsites(tree, reference = NULL, gapChar = "-", minSNP = NULL) ## S3 method for class 'lineagePath' fixationSites(paths, reference = NULL, gapChar = "-", tolerance = 0.01, minEffectiveSize = NULL, extendedSearch = TRUE, ...) ## S3 method for class 'lineagePath' multiFixationSites(paths, reference = NULL, gapChar = "-", minEffectiveSize = NULL, extendedSearch = TRUE, ...)
tree |
The return from |
reference |
Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering |
gapChar |
The character to indicate gap. The numbering will skip the gapChar for the reference sequence. |
minSNP |
Minimum number of amino acid variation to be a SNP |
paths |
a |
tolerance |
A vector of two integers to specify maximum amino acid variation 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 maximum. If only given one number, it's the maximum for both ancestral and descendant. The default is 0.01 |
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. |
extendedSearch |
Whether to extend the search. The terminal of each |
... |
further arguments passed to or from other methods. |
SNPsite
returns a list of qualified SNP site
fixationSites
returns a list of mutations
with names of the tips involved. The name of each list element
is the discovered mutation. A mutation has two vectors of tip names:
'from' before the fixation and 'to' after the fixation.
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), tolerance = c(1, 1), minEffectiveSize = c(50, 50) ) data(h3n2_tree_reduced) data(h3n2_align_reduced) tree <- addMSA(h3n2_tree_reduced, alignment = h3n2_align_reduced) multiFixationSites(lineagePath(tree))