getSeqORFs {ORFhunteR} | R Documentation |
Extract the sequences of identified open reading frames.
getSeqORFs(orfs, tr, genome = "BSgenome.Hsapiens.UCSC.hg38", workDir = NULL)
orfs |
character string giving the name of tab-delimited TXT file with coordinates of open reading frame(-s). This file should include three mandatory fields: i) transcript_id - transcript ID; ii) start - start coordinate of open reading frame in a transcript; iii) end - end coordinate of open reading frame in a transcript. |
tr |
character string giving the name of file with transcript(-s) of interest. This file must include the transcript(-s) for which the open reading frame(-s) was/were identified and listed in above orfs file. Valid formats are "gtf", "gff", "fasta" and "fa". |
genome |
character string giving the name of BSgenome data package with full genome sequences. Default value is "BSgenome.Hsapiens.UCSC.hg38". |
workDir |
character string giving the path to and name of work directory. NULL by default that mean the current working directory. |
DNAStringSet object with sequences of extracted open reading frames.
Vasily V. Grinev
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)