Genes {DECIPHER} | R Documentation |
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.
## 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, ...]
x |
An object of class |
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 |
colorBy |
Character string indicating the name of the column in |
colorRamp |
A function that will return |
colorGenes |
Character string specifying the color of genes, or |
i |
Numeric or character vector of row indices to extract from |
j |
Numeric or character vector of column indices to extract from |
... |
Other optional parameters. |
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.
Erik Wright eswright@pitt.edu
ExtractGenes
, FindGenes
, WriteGenes
# 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))