Skip to contents

Identify conserved sites

Source: R/identify_conserved_sites.R
identify_conserved_sites.Rd

Identify conserved sites relative to the founder sequence. Note that the positions returned assume that the start of the alignment is also the start of the founder sequence in the simulation.

Usage

identify_conserved_sites(
  aln,
  founder,
  thresh = 0.99,
  ref = NULL,
  founder_aln = NULL
)

Arguments

aln

Alignment in ape::DNAbin format (e.g. read in with ape::read.dna() or ape::read.FASTA()) that includes the founder sequence or a reference sequence, plus a representative set of sequences for your genome region of interest

founder

Name of the founder sequence in the input alignment or in the optional founder-specific alignment (founder_aln)

thresh

Conserved site threshold. A position is considered to be conserved if >thresh proportion of sequences in the alignment are the same base (default: 0.99)

ref

Name of the reference sequence in the input alignment, required if the founder sequence is not in aln (default: NULL)

founder_aln

Alignment including the reference and founder sequences, required if the founder is not present in aln. NOTE: This alignment and aln are assumed to begin at the same position in the reference sequence (default: NULL)

Value

Tibble including the following columns:

  • founder_pos: founder position

  • founder_base: founder base

  • consensus_base: consensus base

  • consensus_prop: proportion of sequences that had that base at that position

  • conserved: whether or not the position is conserved (Yes means conserved, No means not conserved, NA means the conserved position is a gap ('-')) When using a reference, NA in the consensus columns indicates that that position was an insertion relative to the reference. All positions are indexed at 0.

Examples

gp120_flt_2022 <- slice_aln(hiv_env_flt_2022, start = 1, end = 2517)
gp120_hxb2_cons_founder <- slice_aln(hxb2_cons_founder, start = 6225, end = 7757)
identify_conserved_sites(
  gp120_flt_2022,
  "B.FR.83.HXB2_LAI_IIIB_BRU.K03455"
)
#> # A tibble: 1,023 × 5
#>    founder_pos founder_base consensus_base consensus_prop conserved
#>          <dbl> <chr>        <chr>                   <dbl> <chr>    
#>  1           0 a            a                         1   Yes      
#>  2           1 t            t                         1   Yes      
#>  3           2 g            g                         1   Yes      
#>  4           3 a            a                         1   Yes      
#>  5           4 g            g                         1   Yes      
#>  6           5 a            a                         1   Yes      
#>  7           6 g            g                         1   Yes      
#>  8           7 t            t                         0.8 No       
#>  9           8 g            g                         1   Yes      
#> 10           9 a            a                         1   Yes      
#> # ℹ 1,013 more rows
identify_conserved_sites(gp120_flt_2022,
  "B.US.2011.DEMB11US006.KC473833",
  ref = "B.FR.83.HXB2_LAI_IIIB_BRU.K03455",
  founder_aln = gp120_hxb2_cons_founder
)
#> # A tibble: 1,473 × 5
#>    founder_pos founder_base consensus_base consensus_prop conserved
#>          <dbl> <chr>        <chr>                   <dbl> <chr>    
#>  1           0 a            a                         1   Yes      
#>  2           1 t            t                         1   Yes      
#>  3           2 g            g                         1   Yes      
#>  4           3 a            a                         1   Yes      
#>  5           4 g            g                         1   Yes      
#>  6           5 a            a                         1   Yes      
#>  7           6 g            g                         1   Yes      
#>  8           7 c            t                         0.8 No       
#>  9           8 g            g                         1   Yes      
#> 10           9 a            a                         1   Yes      
#> # ℹ 1,463 more rows