Map a sequence to a vector of numbers (generic ggDNAvis helper)

This function takes a sequence and encodes it as a vector of numbers for visualisation via raster::raster().

Encoding: A = 1, C = 2, G = 3, T/U = 4.

Usage

convert_sequence_to_numbers(sequence, length = NA)

Arguments

sequence

character. A DNA/RNA sequence (A/C/G/T/U) to be encoded numerically. No other characters allowed. Only one sequence allowed.

length

integer. How long the output numerical vector should be. If shorter than the sequence, the vector will include the first n bases up to this length. If longer than the sequence, the vector will be padded with 0s at the end. If left blank/set to NA (default), will output a vector the same length as the input sequence.

Value

integer vector. The numerical encoding of the input sequence, cut/padded to the desired length.

Examples

convert_sequence_to_numbers("ATCGATCG")
#> [1] 1 4 2 3 1 4 2 3
convert_sequence_to_numbers("ATCGATCG", length = NA)
#> [1] 1 4 2 3 1 4 2 3
convert_sequence_to_numbers("ATCGATCG", length = 4)
#> [1] 1 4 2 3
convert_sequence_to_numbers("ATCGATCG", length = 10)
#>  [1] 1 4 2 3 1 4 2 3 0 0