collapse_others() returns a tbl_df summarising
all unique haplotype frequencies, duplicates and selected metadata into a single row.
Arguments
- data
An object of class tbl_df containing sequence metadata.
- hap_tbl
Output from haplotype_tbl.
- labels
Column name which contains sequence names.
- cols
A character vector of variables to collapse.
Value
an object of class tbl_df.
Details
collapse_others() is a helper function to summarise metadata along with
haplotype_tbl. For any given cols, collapse_others() flattens its content
by unique haplotypes and its duplicates in hap_tbl.
Examples
# summarise haplotypes
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
# summarise country
others_df <- collapse_others(geophagus_info, hap_tbl, "gbAccession", "country")