The result of fixationSites
and sitePath
contains all the possible sites with fixation mutation. The function
extractTips
retrieves the name of the tips involved in the fixation.
For lineagePath
, the function extractTips
groups all the tree tips according to the amino acid/nucleotide of the
site
.
For parallelSites
and sitePara
object, the
function extractTips
retrieve all the tips with parallel mutation.
extractTips(x, ...)
# S3 method for lineagePath
extractTips(x, site, ...)
# S3 method for sitesMinEntropy
extractTips(x, site, ...)
# S3 method for fixationSites
extractTips(x, site, select = 1, ...)
# S3 method for sitePath
extractTips(x, select = 1, ...)
# S3 method for parallelSites
extractTips(x, site, ...)
# S3 method for sitePara
extractTips(x, ...)
A fixationSites
or a sitePath
object.
Other arguments
A site predicted to experience fixation.
For a site, there theoretically might be more than one fixation on different lineages. You may use this argument to extract for a specific fixation of a site. The default is the first fixation of the site.
Tree tips grouped as list
data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
mutations <- fixationSites(lineagePath(tree))
extractTips(mutations, 139)
#> [[1]]
#> [1] "ANK57896" "AMD61711" "AQS26698" "APG56458" "AUI42289" "AMR39834"
#> [7] "AWH65848" "APO08504" "AMX81917" "AVZ47169" "AMX81916" "AMD61710"
#> [13] "AMK49492" "AMX81915" "AOC50652" "APH11611" "BBC70847" "AUF35022"
#> [19] "ATL14618" "AUF35021"
#> attr(,"AA")
#> [1] "S"
#>
#> [[2]]
#> [1] "ANO46307" "AVG19275" "ANN44857" "ANO46302" "ANO46301" "AMD16557"
#> [7] "APB03018" "AWH65849" "AMC13911" "APB03019" "ARB07953" "ARU07076"
#> [13] "ARU07074" "AMX81919" "AMB37295" "ANC90426" "ALU33341" "ASB32509"
#> [19] "AMH87239" "AMA12086" "AMA12085" "AMU04506" "AMA12087" "AMA12084"
#> [25] "AOY08538" "AOG18295" "AOY08517" "AOY08541" "AMM39805" "ARX97119"
#> [31] "AMK79468" "AML82110" "AMR39831" "AMX81918" "APY24200" "AOO19564"
#> [37] "AUI42194" "AOG18296" "AQZ41954" "AOY08533" "ATI21641" "ATG29291"
#> [43] "ATG29301" "APO08503" "AOW32303" "AMC13913" "AMC13912" "AOC50654"
#> [49] "ATG29292" "ATG29295" "AOY08536" "ASL68974" "AMQ48986" "ATG29315"
#> [55] "ATG29307" "ATG29270" "AQZ41952" "AQZ41955" "ARI68105" "ASU55505"
#> [61] "AQM74762" "AUD54964" "ART29828" "AWF93617" "APC60215" "ATG29306"
#> [67] "ATG29284" "AQM74761" "ATG29287" "ATG29303" "AWF93619" "AWF93618"
#> attr(,"AA")
#> [1] "N"
#>