go.details {gcExplorer}R Documentation

Functional Group Methods

Description

Plot or extract size, members or data of a functional group

Usage

## S4 method for signature 'data.frame':
go.details(object, mvalues, gn, id, stats, links, gonr,
    source.id, source.group, details = c("size", "names", "id", "data"), 
    table = TRUE, file = "go.details", plot = TRUE, cexl = 0.8, 
    xlab = "", xlabels = NULL, ylab = "M", ylim = c(-6,6), cex.axis = 1, ...)

Arguments

object An object of class "data.frame".
mvalues Vector giving the columns in object which correspond to the gene expression values.
gn Column of object which corresponds to the gene names used for representation.
id Column of object which corresponds to the unique IDs of the same type as given in source.id.
links Column of object which corresponds to links to database.
stats Column(s) of object which correspond to statistics.
gonr Unique identifier from source.group giving the group of genes to be extracted.
source.id Vector of gene IDs assigned to functional groups given in source.group.
source.group Vector of the same length as source.id.
details The type of details to be extracted.
table Logical. Should an html table be created.
file The file where the output of 'gotable' will be written.
plot Logical. Should the genes be plotted.
cexl Point size of the legend.
xlab Label for the x-axis.
xlabels Either a numeric vector of time points giving the positions on the x-axis or a character vector with names of the positions on the x-axis.
ylab Label for the y-axis.
ylim Range of the y-axis.
cex.axis Point size of the axis.
... Further arguments can be passed to matplot or write.htmltable.

Author(s)

Theresa Scharl

See Also

fitsod

Examples

data(fitsod)
data(gobp)

## Plot the functional group
go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26,
        gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1],
        plot = TRUE)

## A file named "go.details.html" will be created in the current 
## working directory.
go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26,
        gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1],
        table = TRUE)

## Names of the genes in functional group "flagellar"
go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26,
        gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1],
        details = "names")

## Gene expression values of the functional group
d1 <- go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26,
        gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1],
        details = "data")
dim(d1)


[Package gcExplorer version 0.9-1 Index]