Retrieve position of all the sites

The function is a way to get position of the resulting sites from SNPsites, fixationSites and parallelSites. The numbering is consistent with what's being set by setSiteNumbering

allSitesName(x, ...)

# S3 method for SNPsites
allSitesName(x, ...)

# S3 method for sitesMinEntropy
allSitesName(x, ...)

# S3 method for fixationSites
allSitesName(x, ...)

# S3 method for parallelSites
allSitesName(x, ...)

# S3 method for paraFixSites
allSitesName(x, type = c("paraFix", "fixation", "parallel"), ...)

Arguments

x

The object containing the sites from analysis

...

Other arguments

type

Return fixation or parallel sites

Value

An integer vector for sites position

Examples

data(zikv_tree)
msaPath <- system.file('extdata', 'ZIKV.fasta', package = 'sitePath')
tree <- addMSA(zikv_tree, msaPath = msaPath, msaFormat = 'fasta')
snp <- SNPsites(tree)
allSitesName(snp)
#>  [1] "80"   "106"  "107"  "109"  "123"  "139"  "196"  "709"  "784"  "894" 
#> [11] "988"  "1118" "1143" "1542" "2074" "2086" "2611" "2634" "2787" "2842"
#> [21] "3045" "3144" "3162" "3190" "3328" "3353" "3398"