findPTCs {ORFhunteR} | R Documentation |
Identify the premature termination codons in nucleotide sequences of interest.
findPTCs(orfs, gtf, workDir = NULL)
orfs |
character string giving the name of tab-delimited TXT file with coordinates of open reading frame(-s). This file should include four 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; iv) length - length of open reading frame. |
gtf |
character string giving the name of GTF/GFF file with annotated transcripts of interest. Valid format is "gtf" or "gff". |
workDir |
character string giving the path to and name of work directory. NULL by default that mean the current working directory. |
data.frame object with start and stop positions, length and stop status of codons for each transcript ID.
Vasily V. Grinev
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)