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")

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