processCapRout {nearBynding} | R Documentation |
Creates context-separated bedGraph files of CapR output for genome and transcriptome alignments.
processCapRout( CapR_outfile, output_prefix, chrom_size, genome_gtf, RNA_fragment, chain )
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 |
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
## 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")