predictORF: Predict the true ORFs in mRNA molecules

In rfctbio-bsu/ORFhunteR: Predict open reading frames in nucleotide sequences

Predict the true ORFs in mRNA molecules

Description

Predict the true ORFs in mRNA molecules.

Usage

predictORF(
  tr,
  genome = "BSgenome.Hsapiens.UCSC.hg38",
  model = NULL,
  prThr = 0.5,
  workDir = NULL
)

Arguments

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.

Value

The coordinates of ORFs in mRNA molecules of interest.

Author(s)

Mikalai M. Yatskou

Examples

## 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)

rfctbio-bsu/ORFhunteR documentation built on July 16, 2024, 10:40 a.m.