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"
#>