Assessment {AssessORF} | R Documentation

## Assessment objects

### Description

In order to assess the quality of a set of (predicted) genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for that gene or against that gene. Class `Assessment` furnishes objects that can store the neccesary information for assessing a set of genes for a genome and also provides functions for viewing and visualizing assessment information. Specifically, class `Assessment` objects utilize proteomic hits and evolutionarily conserved start & stop codons as evidence to determine the correctness for each gene in a given set.

### `DataMap` Objects

Objects of class `Assessment` and subclass `DataMap` are used to store the mapping of proteomics and evolutionary conservation to the genome of interest (central genome). They are generated through the function `MapAssessmentData`, and they have a list structure containing the following elements:

`StrainID`

  Equal to `strainID` if it was specified; otherwise ""

`Species`

  Equal to `speciesName` if it was specified; otherwise ""

`GenomeLength`

  Length of the central genome

`StopsByFrame`

  Where the stops are in each frame, used to bound open reading frames in downstream functions

`N-TermProteomics`

  Logical describing whether or not the proteomics hits are from N-terminal proteomics

`FwdProtHits`

  Proteomic hit information that maps to the three forward frames of the central genome

`RevProtHits`

  Proteomic hit information that maps to the three reverse frames of the central genome

`FwdCoverage`

  Coverage of the forward strand of the central genome

`FwdConStarts`

  Start codon conservation of the forward strand of the central genome

`FwdConStops`

  Stop codon conservation of the forward strand of the central genome

`RevCoverage`

  Coverage of the reverse strand of the central genome

`RevConStarts`

  Start codon conservation of the reverse strand of the central genome

`RevConStops`

  Stop codon conservation of the reverse strand of the central genome

`NumRelatedGenomes`

  Number of related genomes that were mapped to the central genome

`HasProteomics`

  Logical describing whether or not proteomics evidence has been mapped to the central genome

`HasConservation`

  Logical describing whether or not evolutionary conservation evidence has been mapped to the central genome

### `Results` Objects

Objects of class `Assessment` and subclass `Results` are used to store how correct a set of genes for a given genome. The function `AssessGenes` generates `Results` using a `DataMap` object and information on a set of genes for the genome corresponding to the `DataMap` object. `Results` objects have a list structure containing the following elements:

`StrainID`

  Equal to the `strainID` of the corresponding `DataMap` object

`Species`

  Equal to `speciesName` of the corresponding `DataMap` object

`GenomeLength`

  Length of the genome

`GeneLeftPos`

  Left positions of the given set of genes (in forward strand terms)

`GeneRightPos`

  Right positions of the given set of genes (in forward strand terms)

`GeneStrand`

  Strand information of the given set of genes ("+" or "-")

`GeneSource`

  The source of the given set of genes

`NumGenes`

  Number of genes given

`N_CS-_PE+_ORFs`

  Data for open reading frames with no gene start but with proteomics evidence

`N_CS+_PE+_ORFs`

  Data for open reading frames with no gene start but with proteomics evidence and at least one valid evolutionarily conserved start

`CategoryAssignments`

  A character vector that stores the category assignment for each of the given genes in the same order as the gene information (please see below for a list of all possible categories, their descriptions, and their character string codes)

### Gene Categories

The `CategoryAssignments` vector in `Results` objects describes how the proteomics evidence and evolutionarily conserved start/stop codon evidence support or disprove the corresponding set of genes. In the vector, each gene is assigned a character string code that has the following format: "Y CS[_] PE[_]". The first part, the "Y", signifies that for this ORF contains a predicted gene. The second part, the "CS[_]", describes how the conserved start(s) lines up with the given gene start. The third part, the "PE[_]", describes how the proteomics hits line up with the given gene start.

`Y CS+ PE+`

  There is a good conserved start aligned with the gene start with protein evidence downstream.

`Y CS+ PE-`

  There is a good conserved start aligned with the gene start without protein evidence downstream.

`Y CS- PE+`

  There is no good conserved start aligned with the predicted start, and there is protein evidence downstream of the gene start.

`Y CS- PE-`

  There is no good conserved start aligned with the predicted start, and there is no protein evidence downstream of the gene start.

`Y CS! PE-`

  There are either multiple good conserved stops in the middle of the gene, or the most downstream, good conserved stop is followed by a good conserved start. There is no protein evidence downstream of the gene start

`Y CS! PE+`

  The most downstream, good conserved stop is followed by a good conserved start, and there is protein evidence downstream of the gene start.

`Y CS< PE!`

  The protein evidence disagrees with/is upstream of the gene start, and there is a good conserved start upstream of the protein evidence.

`Y CS- PE!`

  The protein evidence disagrees with/is upstream of the gene start, and there is no good conserved start upstream of the protein evidence.

`Y CS> PE+`

  The best conserved starts are downstream of the predicted start, and there is protein evidence downstream of the gene start.

`Y CS> PE-`

  The best conserved starts are downstream of the predicted start, and there is no protein evidence downstream of the gene start.

`Y CS< PE+`

  At least one of the best conserved starts is upstream of the predicted start, and there is protein evidence downstream of the gene start.

`Y CS< PE-`

  At least one of the best conserved starts is upstream of the predicted start, and there is no protein evidence downstream of the gene start.

### S3 Methods

`as.matrix.Assessment` (only works with objects of class `Results`)

`print.Assessment`

`plot.Assessment`

`mosaicplot.Assessment` (only works with objects of class `Results`)

[Package AssessORF version 1.0.2 Index]