ExtractTranscriptomeSequence: ExtractTranscriptomeSequence

In vbusa1/nearBynding: Discern RNA structure proximal to protein binding

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")

vbusa1/nearBynding documentation built on Aug. 4, 2021, 4:08 p.m.