R: Mean zscore on 242 complete bacterial chromosomes

dinucl {seqinr} | R Documentation

## Mean zscore on 242 complete bacterial chromosomes

### Description

This dataset contains the mean zscores as computed on all intergenic sequences (intergenic) and on all CDS (coding) from 242 complete bacterial chromosomes (as retrieved from Genome Reviews database on June 16, 2005).

### Usage

    data(dinucl)

### Format

List of two dataframes of 242 chromosomes and 16 dinucleotides: one for intergenic, one for coding sequences.

intergenic

  the mean of `zscore` computed with the `base` model on each intergenic sequence

coding

  the mean of `zscore` computed with the `codon` model on each coding sequence

### References

Palmeira, L., Guéguen, L. and Lobry JR. (2006) UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219.
http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214

`citation("seqinr")`

### See Also

`zscore`

### Examples

    data(dinucl)
    par(mfrow = c(2, 2), mar = c(4,4,0.5,0.5)+0.1)
    myplot <- function(x){
      plot(dinucl$intergenic[, x], dinucl$coding[, x],
      xlab = "intergenic", ylab = "coding",
      las = 1, ylim = c(-6, 4),
      xlim = c(-3, 3), cex = 0)
      rect(-10,-10,-1.96,10,col="yellow", border = "yellow")
      rect(1.96,-10,10,10,col="yellow", border = "yellow")
      rect(-10,-10,10,-1.96,col="yellow", border = "yellow")
      rect(-10,1.96,10,10,col="yellow", border = "yellow")
      abline(v=0,lty=3)
      abline(h=0,lty=3)
      abline(h=-1.96,lty=2)
      abline(h=+1.96,lty=2)
      abline(v=-1.96,lty=2)
      abline(v=+1.96,lty=2)
      points(dinucl$intergenic[, x], dinucl$coding[, x], pch = 21,
      col = rgb(.1,.1,.1,.5), bg = rgb(.5,.5,.5,.5))
      legend("bottomright", inset = 0.02,
       legend = paste(substr(x,1,1), "p",
        substr(x,2,2), " bias", sep = ""), cex = 1.25, bg = "white")
      box()
    }
    myplot("CT")
    myplot("TC")
    myplot("CC")
    myplot("TT")

[Package seqinr version 3.4-5 Index]