ExtractTranscriptomeSequence {nearBynding} | R Documentation

## ExtractTranscriptomeSequence

### Description

Writes a FASTA file of transcript sequences from a list of transcripts.

### Usage

    ExtractTranscriptomeSequence(
      transcript_list,
      ref_genome,
      genome_gtf,
      RNA_fragment = "exon",
      exome_prefix = "exome"
    )

### Arguments

`transcript_list` | A vector of transcript names that represent the most expressed isoform of their respective genes and correspond to GTF annotation names. Required
`ref_genome` | The name of the reference genome FASTA from which exome sequences will be derived; a string. Required
`genome_gtf` | The name of the GTF/GFF file that contains all exome annotations; a string. Coordinates must match the file input for the ref_genome parameter. Required
`RNA_fragment` | A string of RNA component of interest. Options depend on the gtf file but often include "gene", "transcript", "exon", "CDS", "five_prime_utr", and/or "three_prime_utr". Default "exon" for the whole exome.
`exome_prefix` | A string to add to the prefix for all output files. Default "exome"

### Value

writes FASTA file of transcriptome sequences into directory

### Note

transcript_list, genome_gtf, and RNA_fragment arguments should be the same as GenomeMappingToChainFile function arguments

### Examples

    ## load transcript list
    load(system.file("extdata/transcript_list.Rda", package="nearBynding"))
    ##get GTF file
    gtf<-system.file("extdata/Homo_sapiens.GRCh38.chr4&5.gtf",
                     package="nearBynding")
    ExtractTranscriptomeSequence(transcript_list = transcript_list,
                 ref_genome = "Homo_sapiens.GRCh38.dna.primary_assembly.fa",
                 genome_gtf = gtf,
                 RNA_fragment = "three_prime_utr",
                 exome_prefix = "chr4and5_3UTR")

[Package nearBynding version 1.2.0 Index]