evalModel {pram} | R Documentation

## Evaluate transcript model

### Description

Evaluate trascript model's precision and recall on exon nucleotides, splice junctions, and splice patterns by comparing them to transcript targets

### Usage

    evalModel(model_exons, target_exons)

    ## S4 method for signature 'GRanges,GRanges'
    evalModel(model_exons, target_exons)

    ## S4 method for signature 'character,character'
    evalModel(model_exons, target_exons)

    ## S4 method for signature 'data.table,data.table'
    evalModel(model_exons, target_exons)

    ## S4 method for signature 'character,data.table'
    evalModel(model_exons, target_exons)

### Arguments

`model_exons` | genomic coordinates for transcript model exons
`target_exons` | genomic coordinates for transcript target exons

### Value

a data table of precision, recall, number of true positive, false negative, false positive for all three evaluated features

### Methods (by class)

- `model_exons = GRanges,target_exons = GRanges`: Both model_exons and target_exons are GRanges objects to define genomic coordinates of exons. Required to have a meta-data column named 'trid' to define each exon's transcript ID.

- `model_exons = character,target_exons = character`: Both model_exons and target_exons are GTF files with full names. Each GTF file is required to have a 'transcript_id' tag in column 9.

- `model_exons = data.table,target_exons = data.table`: Both model_exons and target_exons are data.table objects to define exon genomic coordinatess. Required to have the following columns:

  - chrom: exon's chromosome, e.g. 'chr8'

  - start: exon's start position

  - end: exon's end position

  - strand: exon's strand, '+' or '-'

  - trid: exon's transcript ID

- `model_exons = character,target_exons = data.table`: The model_exons is a GTF file with full name and target_exons is a data.table object. Requirements for GTF and data.table are the same as above

### Examples

    fmdl = system.file('extdata/benchmark/plcf.tsv', package='pram')
    ftgt = system.file('extdata/benchmark/tgt.tsv',  package='pram')

    mdldt = data.table::fread(fmdl, header=TRUE, sep="\t")
    tgtdt = data.table::fread(ftgt, header=TRUE, sep="\t")

    evalModel(mdldt, tgtdt)

[Package pram version 1.4.0 Index]