## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(nearBynding) library(Rsamtools) ## ----echo=FALSE--------------------------------------------------------------- ## test whether the local computer can run the required programs bedtools<-suppressWarnings(system2("bedtools", "--version", stdout = NULL, stderr = NULL)) == 0 CapR<-suppressWarnings(system2("CapR", stdout = NULL, stderr = NULL)) == 0 stereogene<-suppressWarnings(system2("Stereogene", "-h", stdout = NULL, stderr = NULL)) == 0 ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("nearBynding") ## ----eval=FALSE--------------------------------------------------------------- # cd CapR-master # make # ./CapR ## ----eval=FALSE--------------------------------------------------------------- # cd stereogene-master # cd src # make # ./stereogene -h ## ----------------------------------------------------------------------------- # load 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") GenomeMappingToChainFile(genome_gtf = gtf, out_chain_name = "test.chain", RNA_fragment = "three_prime_utr", transcript_list = transcript_list, alignment = "hg38") ## ----------------------------------------------------------------------------- getChainChrSize(chain = "test.chain", out_chr = "chr4and5_3UTR.size") ## ----eval = FALSE------------------------------------------------------------- # 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") ## ----------------------------------------------------------------------------- chr4and5_3UTR.fa <- system.file("extdata/chr4and5_3UTR.fa", package="nearBynding") ## ----eval = CapR-------------------------------------------------------------- # runCapR(in_file = chr4and5_3UTR.fa) ## ----eval = bedtools---------------------------------------------------------- # bam <- system.file("extdata/chr4and5.bam", package="nearBynding") # sorted_bam<-sortBam(bam, "chr4and5_sorted") # # CleanBAMtoBG(in_bam = sorted_bam) ## ----------------------------------------------------------------------------- liftOverToExomicBG(input = "chr4and5_sorted.bedGraph", chain = "test.chain", chrom_size = "chr4and5_3UTR.size", output_bg = "chr4and5_liftOver.bedGraph") ## ----------------------------------------------------------------------------- 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") ## ----eval = stereogene-------------------------------------------------------- # runStereogeneOnCapR(protein_file = "chr4and5_liftOver.bedGraph", # chrom_size = "chr4and5_3UTR.size", # name_config = "chr4and5_3UTR.cfg", # input_prefix = "chr4and5_3UTR") ## ----echo = FALSE, eval = !stereogene, results='hide'------------------------- get_outfiles() ## ----eval = FALSE------------------------------------------------------------- # runStereogene(track_files = c("chr4and5_3UTR_stem_liftOver.bedGraph", # "chr4and5_liftOver.bedGraph"), # name_config = "chr4and5_3UTR.cfg") ## ----eval = stereogene-------------------------------------------------------- # visualizeCapRStereogene(CapR_prefix = "chr4and5_3UTR", # protein_file = "chr4and5_liftOver", # heatmap = TRUE, # out_file = "all_contexts_heatmap", # x_lim = c(-500, 500)) # visualizeCapRStereogene(CapR_prefix = "chr4and5_3UTR", # protein_file = "chr4and5_liftOver", # x_lim = c(-500, 500), # out_file = "all_contexts_line", # y_lim = c(-18, 22)) ## ----fig.show='hold', echo = FALSE, out.width = '50%'------------------------- knitr::include_graphics("all_contexts_heatmap.jpeg") knitr::include_graphics("all_contexts_line.pdf") ## ----eval = stereogene-------------------------------------------------------- # visualizeStereogene(context_file = "chr4and5_3UTR_stem_liftOver", # protein_file = "chr4and5_liftOver", # out_file = "stem_line", # x_lim = c(-500, 500)) # visualizeStereogene(context_file = "chr4and5_3UTR_stem_liftOver", # protein_file = "chr4and5_liftOver", # heatmap = TRUE, # out_file = "stem_heatmap", # x_lim = c(-500, 500)) ## ----fig.show='hold', echo = FALSE, out.width = '50%'------------------------- knitr::include_graphics("stem_heatmap.jpeg") knitr::include_graphics("stem_line.pdf") ## ----------------------------------------------------------------------------- bindingContextDistance(RNA_context = "chr4and5_3UTR_stem_liftOver", protein_file = "chr4and5_liftOver", RNA_context_2 = "chr4and5_3UTR_hairpin_liftOver") ## ----------------------------------------------------------------------------- bindingContextDistance(RNA_context = "chr4and5_3UTR_internal_liftOver", protein_file = "chr4and5_liftOver", RNA_context_2 = "chr4and5_3UTR_hairpin_liftOver") ## ----------------------------------------------------------------------------- sessionInfo()