get_alignment_score: Calculate score of each site in alignment

In Busydog1990/genepro: CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences

Calculate score of each site in alignment

Description

Calculate score of each site in alignment

Usage

get_alignment_score(
  alignment = NULL,
  alignment_file = NULL,
  standard = F,
  symbol = "site",
  type = c("DNA", "RNA", "AA"),
  seq_length_limit = 0L,
  remove_duplicated = F
)

Arguments

alignment	input sequence alignment result, for DNA/RNA/protein sequences, DNAStringSet/RNAStringSet/AAStringSet or character class were required. All sequences must have the same length.
alignment_file	the path of input sequence alignment result.
standard	Logical. If TRUE, Only keep the score of AA_STANDARD/DNA_BASES/RNA_BASES for protein/DNA/RNA sequences. Default:FALSE.
symbol	Character. Prefix of colnames of result. Default:"site".
type	Input sequence type.One of "DNA", "RNA" or "AA".
seq_length_limit	Integer. Lower limit of input sequence length. Default:0.
remove_duplicated	Logical. If TRUE, only one sequence with repeated names in the score matrix is kept. Default:FALSE.

Value

score matrix of each site. rownames of the repeated sequence name will be suffixed.

Examples

require(ggseqlogo)
data(ggseqlogo_sample)
test_aa <- get_alignment_score(alignment = seqs_aa[[1]],type = "AA")
test_dna <- get_alignment_score(alignment = seqs_dna[[1]],type = "DNA")

Busydog1990/genepro documentation built on July 20, 2023, 6:03 a.m.