ExtractTranscriptomeSequence: ExtractTranscriptomeSequence

In 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")

nearBynding documentation built on Nov. 8, 2020, 8:15 p.m.