GenomeMappingToChainFile {nearBynding} | R Documentation

## GenomeMappingToChainFile

### 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")

[Package nearBynding version 1.0.0 Index]