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Map reference and founder sequence positions

Source: R/identify_conserved_sites.R
map_ref_founder.Rd

Map reference and founder sequence positions

Usage

map_ref_founder(aln, ref, founder)

Arguments

aln

Alignment in ape::DNAbin format (e.g. read in with ape::read.dna() or ape::read.FASTA()) that includes the reference sequence and the founder sequence

ref

Name of the reference sequence in the input alignment

founder

Name of the founder sequence in the input alignment

Value

Tibble including columns for:

  • Alignment position (alignment_pos)

  • Reference base position (ref_pos)

  • Founder base position (founder_pos)

  • Reference base (ref_base)

  • Founder base (founder_base) All positions are indexed at 0.

Examples

map_ref_founder(
  hxb2_cons_founder,
  "B.FR.83.HXB2_LAI_IIIB_BRU.K03455",
  "B.US.2011.DEMB11US006.KC473833"
)
#> # A tibble: 9,022 × 5
#>    alignment_pos ref_pos founder_pos ref_base founder_base
#>            <dbl>   <dbl>       <dbl> <chr>    <chr>       
#>  1           646     646           0 c        c           
#>  2           647     647           1 a        a           
#>  3           648     648           2 g        g           
#>  4           649     649           3 g        g           
#>  5           650     650           4 g        g           
#>  6           651     651           5 a        a           
#>  7           652     652           6 c        c           
#>  8           653     653           7 c        t           
#>  9           654     654           8 t        t           
#> 10           655     655           9 g        g           
#> # ℹ 9,012 more rows