GenomeMappingToChainFile {nearBynding} | R Documentation |
Writes a chain file mapped from a genome annotation file.
GenomeMappingToChainFile( genome_gtf, out_chain_name, RNA_fragment = "exon", transcript_list, chrom_suffix = "exome", verbose = FALSE, alignment = "hg19", check_overwrite = FALSE )
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. |
writes a chain file into directory
## 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")