getChainChrSize {nearBynding} | R Documentation |
Output a table of mapped chromosome names and lengths from a chain file.
getChainChrSize(chain, out_chr)
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. |
writes a two-column tab-delineated file without a header containing chromosome names and lengths for a given chain file
## 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")