getChainChrSize {nearBynding} | R Documentation

## getChainChrSize

### Description

Output a table of mapped chromosome names and lengths from a chain file.

### Usage

    getChainChrSize(chain, out_chr)

### Arguments

`chain` | The name of the chain file for which chromosome sizes should be determined and output; a string. Required.
`out_chr` | Name of the chromosome names and lengths table file; a string. Required.

### Value

writes a two-column tab-delineated file without a header containing chromosome names and lengths for a given chain file

### Examples

    ## first, make the chain file
    load(system.file("extdata/transcript_list.Rda", package="nearBynding"))
    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")

    getChainChrSize(chain = "test.chain",
                   out_chr = "chr4and5_3UTR.size")

[Package nearBynding version 1.4.0 Index]