GenomeMappingToChainFile: GenomeMappingToChainFile

In nearBynding: Discern RNA structure proximal to protein binding

Description

Writes a chain file mapped from a genome annotation file.

Usage

GenomeMappingToChainFile(
    genome_gtf,
    out_chain_name,
    RNA_fragment = "exon",
    transcript_list,
    chrom_suffix = "exome",
    verbose = FALSE,
    alignment = "hg19",
    check_overwrite = FALSE
)

Arguments

genome_gtf	The name of the GTF/GFF file that will be converted to an exome chain file. Required
out_chain_name	The name of the chain file to be created. Required
RNA_fragment	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.
transcript_list	A vector of transcript names that represent the most expressed isoform of their respective genes and correspond to gtf annotation names. Isoforms cannot overlap. Required
chrom_suffix	The suffix to be appended to all chromosome names created in the chain file. Default "exome"
verbose	Output updates while the function is running. Default FALSE
alignment	The human genome alignment used, either "hg19" or "hg38". Default "hg19"
check_overwrite	Check for file wth the same out_chain_name before writing new file. Default FALSE.

Value

writes a chain file into directory

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")

GenomeMappingToChainFile(genome_gtf = gtf,
                        out_chain_name = "test.chain",
                        RNA_fragment = "three_prime_utr",
                        transcript_list = transcript_list,
                        alignment = "hg38")

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