liftOverToExomicBG {nearBynding} | R Documentation |
Lifts features such as CLIP-seq reads or RNA structure annotations from genome to transcriptome.
liftOverToExomicBG(input, chain, chrom_size, output_bg, format = "bedGraph")
input |
A single input file name or a vector of input file names in the format of c(forward_reads, reverse_reads) for strand-separated alignments. Files must be BED or bedGraph format. Required |
chain |
The name of the chain file to be used for liftOver. Format should be like chain files derived from getChainChrSize function. Required |
chrom_size |
Name of chromosome size file. File must be in two-column format without a header where first column is chromosome name and second column is chromosome length, as from liftOverToExomicBG. Required. |
output_bg |
The name of the lifted-over output bedGraph file. Required. |
format |
File type of input file(s). Recommended "BED" or "bedGraph". Default "bedGraph" |
writes lifted-over bedGraph file
## first, get 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") ## and chain file chromosome sizes getChainChrSize(chain = "test.chain", out_chr = "chr4and5_3UTR.size") ## get bedGraph file chr4and5_sorted.bedGraph<-system.file("extdata/chr4and5_sorted.bedGraph", package="nearBynding") liftOverToExomicBG(input = chr4and5_sorted.bedGraph, chain = "test.chain", chrom_size = "chr4and5_3UTR.size", output_bg = "chr4and5_liftOver.bedGraph")