topTable: Print or plot the top connected miRNA/mRNA

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Print or plot the top connected miRNA/mRNA

Usage

topTable(obj, class, pval.cutoff = 0.05, dat.sum =
    obj@info[["dat.sum"]], score.cutoff = NULL, plot = FALSE,
    names = FALSE, n = NULL, remove.names = FALSE, table.items = NULL)

Arguments

obj	corObject
class	"miRNA" or "mRNA".
pval.cutoff	p value to cutoff.
dat.sum	number of minimum ocurrences across databases.
score.cutoff	maximum score allowed
plot	FALSE or TRUE.
names	FALSE or TRUE. Apart from the frequence, add the names of the hits. (In this case the object returned is a data.frame).
n	maximum number of pairs to consider.
remove.names	in case of a plot, omit x-axis labels.
table.items	when names=TRUE, number of items to be included on the table.

Details

If plot=FALSE then the table is displayed, if plot=TRUE the table is not displayed and a barplot is plotted. If names=FALSE a vector is returned, if names=TRUE, a data.frame is returned.

Value

A data.frame

See Also

plotHeatmap

Examples

data(data.obj)

# get the names
topTable(data.obj, "miRNA", names=TRUE, plot=FALSE)
topTable(data.obj, "mRNA", names=TRUE, plot=FALSE)

# plot
topTable(data.obj, "miRNA", names=TRUE, plot=TRUE)

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.