## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- trans <- system.file("extdata", "Set.trans_sequences.fasta", package = "ORFhunteR") ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("ORFhunteR") ## ----echo=T, results = 'hide'------------------------------------------------- library('ORFhunteR') ## ----------------------------------------------------------------------------- seq.set <- loadTrExper(tr = trans) ## ----------------------------------------------------------------------------- x <- "AAAATGGCTGCGTAATGCAAAATGGCTGCGAATGCAAAATGGCTGCGAATGCCGGCACGTTGCTACGT" orf <- findORFs(x, codStart="ATG") ## ----echo=FALSE, out.width='75%', fig.align="center"-------------------------- knitr::include_graphics('./Figure_1.jpg') ## ----------------------------------------------------------------------------- feats <- vectorizeORFs(x=DNAStringSet(x="ATGGGCCTCA")) ## ----eval = FALSE------------------------------------------------------------- # ## The files with sequences can be downloaded from SST Center server at www.sstcenter.com/download/ORFhunteR # # fileORFLncRNAs <- "http://www.sstcenter.com/download/ORFhunteR/NCBI_RefSeq_release_109_GRCh38.p12_ORF_candidates_sequences_lncRNAs.fasta.gz" # ORFLncRNAs <- loadTrExper(tr = fileORFLncRNAs) # fileORFmRNAs <- "http://www.sstcenter.com/download/ORFhunteR/NCBI_RefSeq_release_109_GRCh38.p12_ORFs_true_sequences_mRNAs.fasta.gz" # ORFmRNAs <- loadTrExper(tr = fileORFmRNAs) # ## Make the train dataset from N pseudo- and N real ORFs. # N <- 1000 # ORFLncRNAs <- ORFLncRNAs[1:N] # ORFmRNAs <- ORFmRNAs[1:N] # ## Calculate the classification model for the open reading frame. # clt <- classifyORFsCandidates(ORFLncRNAs = ORFLncRNAs, # ORFmRNAs = ORFmRNAs, # pLearn = 0.75, # nTrees = 500, # modelRF = NULL, # workDir = NULL, # showAccuracy = TRUE) ## ----------------------------------------------------------------------------- model <- "http://www.sstcenter.com/download/ORFhunteR/classRFmodel_1.rds" ORFs <- predictORF(tr = trans, model= model, prThr = 0) ## ----------------------------------------------------------------------------- head(ORFs) ## ----echo=FALSE, out.width='75%', fig.align="center"-------------------------- knitr::include_graphics('./Figure_2.jpg') ## ----echo=FALSE, out.width='75%', fig.align="center"-------------------------- knitr::include_graphics('./Figure_3.jpg') ## ----------------------------------------------------------------------------- orfs_path <- system.file("extdata", "Set.trans_ORFs.coordinates.txt", package="ORFhunteR") tr_path <- system.file("extdata", "Set.trans_sequences.fasta", package="ORFhunteR") seq_orfs <- getSeqORFs(orfs = orfs_path, tr = tr_path, genome="BSgenome.Hsapiens.UCSC.hg38", workDir=NULL) ## ----------------------------------------------------------------------------- head(seq_orfs) ## ----------------------------------------------------------------------------- orfs_path <- system.file("extdata", "Set.trans_ORFs.coordinates.txt", package="ORFhunteR") gtf_path <- system.file("extdata", "Set.trans_sequences.gtf", package="ORFhunteR") ptcs <- findPTCs(orfs = orfs_path, gtf = gtf_path, workDir = NULL) ## ----------------------------------------------------------------------------- head(ptcs) ## ----------------------------------------------------------------------------- seq_orf_path <- system.file("extdata", "Set.trans_ORFs.sequences.fasta", package="ORFhunteR") prot_seqs <- translateORFs(seqORFs=seq_orf_path) ## ----------------------------------------------------------------------------- head(prot_seqs) ## ----------------------------------------------------------------------------- orfs_path <- system.file("extdata", "Set.trans_ORFs.coordinates.txt", package="ORFhunteR") tr_path <- system.file("extdata", "Set.trans_sequences.fasta", package="ORFhunteR") gtf_path <- system.file("extdata", "Set.trans_sequences.gtf", package="ORFhunteR") prts_path <- system.file("extdata", "Set.trans_proteins.sequences.fasta", package="ORFhunteR") anno_orfs <- annotateORFs(orfs = orfs_path, tr = tr_path, gtf = gtf_path, prts = prts_path, workDir = NULL) ## ----------------------------------------------------------------------------- head(anno_orfs)