evalModel: Evaluate transcript model

In pliu55/pram: Pooling RNA-seq datasets for assembling transcript models

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)

pliu55/pram documentation built on March 30, 2024, 7:24 p.m.