hap_unite() returns a single tbl_df combining all
results from haplotype_tbl or collapse_others with results from delim_join
or delim_consensus.
Arguments
- hap_tbl
output from haplotype_tbl or collapse_others.
- delim
output from delim_join or delim_consensus.
Value
an object of class tbl_df.
Details
Many functions in this package relies on the usage of unique haplotypes due to
known issues when using identical or duplicated sequences for species delimitation analysis.
Thus, these outputs will very often refer only to unique haplotypes within a given dataset,
which can be determined by using functions like hap_collapse. Assuming that a
duplicated or identical sequence should share the same properties as the first
sequence of the group has, hap_unite() combines the output of haplotype_tbl
with the output of delim_join. Alternativelly, one may use collapse_others and
delim_consensus as well. This output may be used for downstream analysis or
to determine in which cluster a given sequence belongs.
Examples
# get haplotype table
hap_tbl <- 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
# unite
hap_unite(hap_tbl, geophagus_delims)
#> # A tibble: 274 × 12
#> labels n_seqs collapsed abgd asap bgmyc gmyc locmin morph mptp ptp
#> <chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 MZ504318.1 38 MZ504328.… sp1 sp20 sp1 sp1 sp1 sp37 sp38 sp1
#> 2 MZ504540.1 20 MZ504505.… sp16 sp16 sp25 sp27 sp33 sp34 sp16 sp16
#> 3 MZ504420.1 19 MZ504417.… sp3 sp23 sp3 sp32 sp3 sp3 sp23 sp23
#> 4 MZ504488.1 16 MZ504538.… sp16 sp16 sp24 sp24 sp33 sp34 sp16 sp16
#> 5 MZ504484.1 15 MZ504496.… sp16 sp16 sp24 sp24 sp33 sp34 sp16 sp16
#> 6 MZ504462.1 14 MZ504479.… sp6 sp21 sp21 sp21 sp6 sp21 sp21 sp21
#> 7 MZ504375.1 13 MZ504372.… sp2 sp23 sp26 sp26 sp2 sp26 sp23 sp23
#> 8 MZ504535.1 8 MZ504515.… sp16 sp16 sp24 sp24 sp33 sp34 sp16 sp16
#> 9 MZ504393.1 8 MZ504445.… sp3 sp23 sp3 sp31 sp3 sp3 sp23 sp23
#> 10 MZ504400.1 6 MZ504404.… sp3 sp23 sp3 sp32 sp3 sp3 sp23 sp23
#> # ℹ 264 more rows
#> # ℹ 1 more variable: status <chr>