Genes {DECIPHER} | R Documentation

## Genes objects and accessors

### Description

Gene prediction consist of delimiting the boundaries of regions that function as genes within a genome. Class `Genes` provides objects and functions for storing the boundaries of genes and associated information resulting from gene prediction.

### Usage

    ## S3 method for class 'Genes'
    plot(x,
        xlim = c(1, 1e4),
        ylim = c(-100, 500),
        interact = FALSE,
        colorBy="Strand",
        colorRamp=colorRampPalette(c("darkblue", "darkred")),
        colorGenes="green4",
        ...)

    ## S3 method for class 'Genes'
    print(x, ...)

    ## S3 method for class 'Genes'
    x[i, j, ...]

### Arguments

`x` | An object of class `Genes`.
`xlim` | Numeric vector of length 2 specifying the x-axis limits for plotting.
`ylim` | Numeric vector of length 2 specifying the y-axis limits for plotting.
`interact` | Logical determining whether the plot is interactive. If `TRUE`, clicking the plot on the right or left side will scroll one frame in that direction. To end interaction, either right-click, press the escape key, or press the stop button depending on the graphics device in use.
`colorBy` | Character string indicating the name of the column in `x` that should be used for coloring. Unambiguous abbreviations are also permitted.
`colorRamp` | A function that will return `n` colors when given a number `n`. Examples are `rainbow`, `heat.colors`, `terrain.colors`, `cm.colors`, or (the default) `colorRampPalette`.
`colorGenes` | Character string specifying the color of genes, or `NA` to color genes according to `colorBy`.
`i` | Numeric or character vector of row indices to extract from `x`.
`j` | Numeric or character vector of column indices to extract from `x`. If `j` is missing, all columns are included and the returned object will also belong to class `Genes`.
`...` | Other optional parameters.

### Details

Objects of class `Genes` are stored as numeric matrices containing information pertaining to gene predictions. The matrix columns include the index (`"Index"`) of the corresponding sequence in the original genome, the strand (`"Strand"`) where the gene is located (either `"+"` (`0`) or `"-"` (`1`), the beginning (`"Begin"`) and ending (`"End"`) positions of the gene, scores acquired during prediction, and whether (`!= 0`) or not (`0`) the region was predicted to be a gene. Note that the start of the gene is at the beginning position when the strand is `"+"` and end when the strand is `"-"`. By convention, rows with negative values in the `"Gene"` column represent non-coding RNAs and rows with positive values represent protein coding genes.

The `plot` method will show the total score of each prediction along the genome. This is most useful when displaying the result of setting `allScores` to `TRUE` in `FindGenes`. Here, possible genes on either strand will be shown (by default), with the predicted genes highlighted. The beginning (solid) and ending (dashed) positions are denoted by vertical lines. Note that the x-axis is cumulative genome position, and changes between genome sequences indices are demarcated by dashed vertical lines.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`ExtractGenes`, `FindGenes`, `WriteGenes`

### Examples

    # import a test genome
    fas <- system.file("extdata",
    	"Chlamydia_trachomatis_NC_000117.fas.gz",
    	package="DECIPHER")
    genome <- readDNAStringSet(fas)

    x <- FindGenes(genome, allScores=TRUE)
    x
    head(unclass(x)) # the underlying structure

    plot(x) # default coloring by "Strand"
    # color by RBS score (blue is weak/low, red is strong/high)
    plot(x, colorBy="RibosomeBindingSiteScore", colorGenes=NA)
    # color by fraction of times a gene was chosen
    plot(x, colorBy="FractionReps", colorGenes=NA)
    # color by which codon model was selected for each ORF
    plot(x, colorBy="CodonModel", xlim=c(1, 3e4))

[Package DECIPHER version 2.22.0 Index]