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)

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 1.8.0 Index]