liftOverToExomicBG: liftOverToExomicBG
In vbusa1/nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Examples

Lifts features such as CLIP-seq reads or RNA structure annotations from genome to transcriptome.

1	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")