nearBynding-package: Discern RNA structure proximal to protein binding

In nearBynding: Discern RNA structure proximal to protein binding

Description

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.

Details

Package:	nearBynding
Type:	Package
Title:	nearBynding package
Version:	0.99.12
Date:	July 21, 2020`
License:	Artistic-2.0
LazyLoad:	yes
URL:	http://github.com/vbusa1/nearBynding

Author(s)

Veronica Busa [e-mail]

References

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 Also

See the nearBynding package vignette.

Examples

## 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)

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