get_gt_sequences {TAPseq} | R Documentation

## Get genome and transcriptome sequences

### Description

Get DNA sequences of all chromosomes and all annotated transcripts of a genome. This function is used to create the sequences in `createBLASTDb`.

### Usage

    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
    )

### Arguments

`genome` | A `BSgenome` (or `DNAStringSet`) object containing the chromosome sequences to obtain genome and / or transcript sequences.
`annot` | A `GRanges` object containing all exons of transcripts to be considered. If not specified, no transcript sequences will be included in the output fasta file.
`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.

### Value

A `DNAStringSet` object containing the genome and transcriptome sequences.

[Package TAPseq version 0.99.6 Index]