nearBynding {nearBynding} | R Documentation |
nearBynding is a package designed to discern annotated RNA structures at and proximal to the site of protein binding. It allows users to annotate RNA structure contexts via CapR or input their own annotations in BED/bedGraph format and it accomodates protein binding information from CLIP-seq experiments as either aligned CLIP-seq reads or peak-called intervals.
Package: | nearBynding |
Type: | Package |
Title: | nearBynding package |
Version: | 1.3.3 |
Date: | June 1, 2021` |
License: | Artistic-2.0 |
LazyLoad: | yes |
URL: | http://github.com/vbusa1/nearBynding |
Veronica Busa vbusa1@jhmi.edu
StereoGene: | Stavrovskaya, Elena D., Tejasvi Niranjan, Elana J. Fertig, Sarah J. Wheelan, Alexander V. Favorov, and Andrey A. Mironov. “StereoGene: Rapid Estimation of Genome-Wide Correlation of Continuous or Interval Feature Data.” Bioinformatics 33, no. 20 (October 15, 2017): 3158–65. https://doi.org/10.1093/bioinformatics/btx379. |
CapR: | Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, and Hisanori Kiryu. "CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data." Genome Biology, 15, R16. (2014) |
See the nearBynding package vignette.
## Not run: library(nearBynding) library(Rsamtools) # get transcript list load(system.file("extdata/transcript_list.Rda", package="nearBynding")) # get GTF file gtf<-system.file("extdata/Homo_sapiens.GRCh38.chr4&5.gtf", package="nearBynding") # make chain file GenomeMappingToChainFile(genome_gtf = gtf, out_chain_name = "test.chain", RNA_fragment = "three_prime_utr", transcript_list = transcript_list, alignment = "hg38") # get size of chromosomes of chain file getChainChrSize(chain = "test.chain", out_chr = "chr4and5_3UTR.size") # get transcript sequences ExtractTranscriptomeSequence(transcript_list = transcript_list, ref_genome = "Homo_sapiens.GRCh38.dna.primary_assembly.fa", genome_gtf = gtf, RNA_fragment = "three_prime_utr", exome_prefix = "chr4and5_3UTR") # run CapR on extracted sequences runCapR(in_file = "chr4and5_3UTR.fa") # get BAM file of protein binding bam <- system.file("extdata/chr4and5.bam", package="nearBynding") # sort it and convert to bedGraph format sorted_bam<-sortBam(bam, "chr4and5_sorted") CleanBAMtoBG(in_bam = sorted_bam) # lift over protein binding and RNA structure to chain liftOverToExomicBG(input = "chr4and5_sorted.bedGraph", chain = "test.chain", chrom_size = "chr4and5_3UTR.size", output_bg = "chr4and5_liftOver.bedGraph") processCapRout(CapR_outfile = "chr4and5_3UTR.out", chain = "test.chain", output_prefix = "chr4and5_3UTR", chrom_size = "chr4and5_3UTR.size", genome_gtf = gtf, RNA_fragment = "three_prime_utr") # input to StereoGene runStereogeneOnCapR(protein_file = "chr4and5_liftOver.bedGraph", chrom_size = "chr4and5_3UTR.size", name_config = "chr4and5_3UTR.cfg", input_prefix = "chr4and5_3UTR") # visualize protein binding context visualizeCapRStereogene(CapR_prefix = "chr4and5_3UTR", protein_file = "chr4and5_liftOver", heatmap = T, out_file = "all_contexts_heatmap", x_lim = c(-500, 500)) ## End(Not run)