Render a TALE alignment as a matrix

Materialises the rectangular form: one row per array, one column per alignment position, cells holding the requested layer. This is the only place the gapped matrix is built — the long object is the canonical storage.

Usage

# S3 method for class 'tales_msa'
as.matrix(x, value = NULL, gap = NA, ...)

Arguments

x

A tales_msa object.

value

Name of the column to fill cells with. Defaults to the first available of rvd, dom_code.

gap

Value to use for gaps. Defaults to NA.

...

Ignored.

Value

A character matrix with arrays as rows and alignment positions as columns.

See also

Other TALE alignment: is_tales_msa(), tales_align(), tales_consensus(), tales_consensus_match(), tales_msa(), tales_msa_params(), tales_msa_width(), validate_tales_msa()

Examples

aligned <- data.frame(
  array_id = c("A1", "A1", "A1", "A2", "A2"),
  position_in_array = c(1L, 2L, 3L, 1L, 2L),
  alignment_position = c(1L, 2L, 3L, 1L, 3L),
  rvd = c("NTERM", "HD", "CTERM", "NTERM", "CTERM")
)
msa <- tales_msa(aligned)
as.matrix(msa) # gaps as NA
#>    1       2    3      
#> A1 "NTERM" "HD" "CTERM"
#> A2 "NTERM" NA   "CTERM"
as.matrix(msa, gap = "-") # gaps as "-"
#>    1       2    3      
#> A1 "NTERM" "HD" "CTERM"
#> A2 "NTERM" "-"  "CTERM"