processCapRout {nearBynding} | R Documentation

## processCapRout

### Description

Creates context-separated bedGraph files of CapR output for genome and transcriptome alignments.

### Usage

    processCapRout(
        CapR_outfile,
        output_prefix,
        chrom_size,
        genome_gtf,
        RNA_fragment,
        chain
    )

### Arguments

`CapR_outfile` | Name of CapR output file. Required
`output_prefix` | Prefix string to be appended to all output files. 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 getChainChrSize. Required.
`genome_gtf` | The name of the GTF/GFF file that contains all exome annotations. 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.
`chain` | The name of the chain file to be used. Format should be like chain files derived from GRangesMappingToChainFile. Required

### Value

writes bedGraph files of structure signal for each of the six CapR contexts 1) mapped to the genome and 2) lifted-over to the transcriptome

### Examples

    ## make 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")
    ## get chromosome size file
    getChainChrSize(chain = "test.chain",
                    out_chr = "chr4and5_3UTR.size")

    processCapRout(CapR_outfile = system.file("extdata/chr4and5_3UTR.out",
                                                package="nearBynding"),
                    chain = "test.chain",
                    output_prefix = "chr4and5_3UTR",
                    chrom_size = "chr4and5_3UTR.size",
                    genome_gtf = gtf,
                    RNA_fragment = "three_prime_utr")

[Package nearBynding version 1.0.0 Index]