processCapRout: processCapRout

In nearBynding: Discern RNA structure proximal to protein binding

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")

nearBynding documentation built on Nov. 8, 2020, 8:15 p.m.