get_gt_sequences {TAPseq} | R Documentation |
Get DNA sequences of all chromosomes and all annotated transcripts of a genome. This function is
used to create the sequences in createBLASTDb
.
get_gt_sequences( genome, annot = NULL, tx_id = "transcript_id", tx_name = "transcript_name", gene_name = "gene_name", gene_id = "gene_id", include_genome = TRUE, standard_chromosomes = TRUE )
genome |
A |
annot |
A |
tx_id, tx_name, gene_name, gene_id |
(character) Column names in annot metadata containing transcript id, transcript name, gene name and gene id information. These column are mandatory, but can contain internal names (e.g. "transcript-1" or "gene-1"). |
include_genome |
(logical) Specifies whether the genome sequence should be included in the output fasta file. |
standard_chromosomes |
(logical) Specifies whether only standard chromosomes should be included in output genome sequences (e.g. chr1-22, chrX, chrY, chrM for homo sapiens). |
compress |
(logical) Create a gzipped output fasta file. |
A DNAStringSet
object containing the genome
and transcriptome sequences.