predictORF {ORFhunteR} | R Documentation

## 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)

[Package ORFhunteR version 1.2.0 Index]