liftOverToExomicBG {nearBynding} | R Documentation

## liftOverToExomicBG

### Description

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

### Usage

    liftOverToExomicBG(input, chain, chrom_size, output_bg, format = "bedGraph")

### Arguments

`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"

### Value

writes lifted-over bedGraph file

### Examples

    ## 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")

[Package nearBynding version 1.0.0 Index]