A utility function from ProGenExpress which prints the data for a genomic region to the screen and draws a plot of that region

show.region(ProGenExpress)

R Documentation

A utility function from ProGenExpress which prints the data for a genomic region to the screen and draws a plot of that region

Description

Usage

show.region(linked = NULL, start = NULL, stop = NULL, 
                cnames = "M", pad = 5000, distscale = 50)

Arguments

`linked`	A data frame consisting of gene names, locations on the genome and numerical values to be plotted. Must have numerical columns "Start" and "Stop" indicating the location on the genome of genes or features
`start`	The Synonym name for the first gene to be plotted
`stop`	The Synonym name for the last gene to be plotted
`cnames`	Vector of column names in linked which contain the numerical values to be plotted
`pad`	A numerical value - number of bases beyond start and stop to encompass
`distscale`	Controls whether or not the distance between groups of bars should represent intergenic distance. If set to NULL, intergenic distance is ignored and groups of bars are plotted equally spaced on the genome. If set to any other value than NULL, intergenic distance is taken into account. If not NULL, the distance between genes A and B is set to: ((number bp between A and B) / distscale) + 1, where the unit is the width of one bar. This ensures that there is always a gap of at least 1 between groups of bars representing distinct genes. A low value of distscale will really emphasize the intergenic distance, whereas a high value will not. A value between 10 and 100 is reccomended for most prokaryotic genomes, although as with most things, this is a matter of preference. Defaults to NULL.

Value

The data for the region is printed to the screen and a plot is drawn

Author(s)

Michael Watson

Examples


        # load the IFR microarray data
        data(IFR)

        # read in an NCBI .ptt file for S typhimurium
        data(STLT2) # produced by 'STLT2 <- read.ptt("NC_003197.ptt")'

        # link the genome and the microarray data on Synonym columns
        # we want one value per gene and so we average over the values
        linked <- linkem.avg(STLT2,IFR,"Synonym","Synonym",cnames=c("M4h","M8h","M12h"))

        # find interesting regions
        reg <- find.region(linked, cnames=c("M4h","M8h","M12h"))

        # examine the first region
        show.region(linked,start=reg[1,1],stop=reg[1,2], cnames=c("M4h","M8h","M12h"))

[Package ProGenExpress version 1.0 Index]