GenomeMappingToChainFile: GenomeMappingToChainFile

Description Usage Arguments Value Examples

View source: R/GenomeMappingToChainFile.R

Description

Writes a chain file mapped from a genome annotation file.

Usage

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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

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## 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")

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