predictORF {ORFhunteR} | R Documentation |
Predict the true ORFs in mRNA molecules.
predictORF( tr, genome = "BSgenome.Hsapiens.UCSC.hg38", model = NULL, prThr = 0.5, workDir = NULL )
tr |
character string giving the name of file with experimental transcripts. Allowed file formats are "fasta", "fa", "gtf" or "gff". |
genome |
character string giving the name of BSgenome data package with full genome sequences. Default value is "BSgenome.Hsapiens.UCSC.hg38". |
model |
character string giving the connection or full path to the file from which the classification model is read. Use default NULL value to use our default model. |
prThr |
probability threshold for the "winning" class of ORFs. Default value is 0.5. |
workDir |
character string giving the path to and name of work directory. NULL by default that mean the current working directory. |
The coordinates of ORFs in mRNA molecules of interest.
Mikalai M. Yatskou
## Not run: tr_path <- system.file("extdata", "Set.trans_sequences.fasta", package="ORFhunteR") model <- "http://www.sstcenter.com/download/ORFhunteR/classRFmodel_1.rds" ORFs <- predictORF(tr=tr_path, model=model) ## End(Not run)