haplotype_tbl() returns a tbl_df summarising
all unique haplotype frequencies and duplicates into a single row.
Arguments
- dna
an object of class DNAbin.
- clean
logical. Whether to remove or not remove non ACTG bases from alignment.
- collapseSubstrings
logical. Whether to collapse or not collapse shorter but identical sequences.
- verbose
logical. Returns a warning if any sequence contains non ACTG bases. See clean_dna for details.
Value
an object of class tbl_df.
Details
haplotype_tbl() uses a combination of clean_dna and hap_collapse to summarise
haplotypes into a tibble. Each row of the tibble has an unique haplotype,
its frequency and all its collapsed duplicates in a flattened string.
Examples
# get haplotype table
haplotype_tbl(geophagus)
#> Warning: ⚠ You have missing data "('N','-' '?')" or ambiguity inside your sequence, i.e.
#> not padding the ends, and this may have unintended consequences later, as they
#> have now been removed!
#> ℹ The names of the samples are bellow.
#> GU701784.1, GU701785.1
#> # A tibble: 137 × 3
#> labels n_seqs collapsed
#> <chr> <dbl> <chr>
#> 1 MZ504318.1 38 MZ504328.1, MZ504313.1, MZ504311.1, MZ504312.1, MZ504309.1…
#> 2 MZ504540.1 20 MZ504505.1, MZ504553.1, MZ504554.1, MZ504552.1, MZ504542.1…
#> 3 MZ504420.1 19 MZ504417.1, MZ504437.1, MZ504425.1, MZ504427.1, MZ504422.1…
#> 4 MZ504488.1 16 MZ504538.1, KU568830.1, JN026709.1, MZ504522.1, MZ504523.1…
#> 5 MZ504484.1 15 MZ504496.1, MZ504487.1, MZ504573.1, MZ504560.1, MZ504497.1…
#> 6 MZ504462.1 14 MZ504479.1, MZ504477.1, MZ504481.1, MZ504476.1, MZ504463.1…
#> 7 MZ504375.1 13 MZ504372.1, MZ504382.1, MZ504381.1, MZ504379.1, MZ504383.1…
#> 8 MZ504535.1 8 MZ504515.1, MZ504525.1, MZ504533.1, MZ504534.1, MZ504536.1…
#> 9 MZ504393.1 8 MZ504445.1, MZ504413.1, MZ504407.1, MZ504408.1, MZ504410.1…
#> 10 MZ504400.1 6 MZ504404.1, MZ504401.1, MZ504402.1, MZ504403.1, MZ504399.1
#> # ℹ 127 more rows