Get one-hot encoded sequences

Source: R/prepare_data_from_FASTA.R

Get the one-hot encoding representation of the given sequences.

get_one_hot_encoded_seqs(seqs, sinuc_or_dinuc = "sinuc")

Arguments

seqs

A DNAStringSet object holding the given DNA sequences
sinuc_or_dinuc

character string, 'sinuc' or 'dinuc' to select for mono- or dinucleotide profiles.

Value

A sparse matrix of sequences represented with one-hot-encoding

See also

prepare_data_from_FASTA for generating one-hot encoding of sequences from a FASTA file

Other input functions: prepare_data_from_FASTA()

Examples


fname <- system.file("extdata", "example_data.fa", 
                        package = "archR", mustWork = TRUE)

                        
rawSeqs <- prepare_data_from_FASTA(fasta_fname = fname,
                        raw_seq = TRUE)

seqs_dinuc <- get_one_hot_encoded_seqs(seqs = rawSeqs, 
                                       sinuc_or_dinuc = "dinuc")

#> Generating dinucleotide profiles