getMain: get main effects

In RNAinteract: Estimate Pairwise Interactions from multidimensional features

Description

Returns the main effects.

Usage

getMain(sgi, type = "main", design = "template", summary = "none",
        QueryNr = NULL, TemplatePlate = NULL, 
	do.inv.trafo = FALSE, format = "plain", withoutgroups = c(), 
	screen = NULL, channel = NULL, normalized = TRUE, drop = TRUE)
getMainNeg(sgi, type = "all", do.inv.trafo = FALSE, 
	screen = NULL, channel = NULL, drop = TRUE)

Arguments

sgi	An object of class RNAinteract
type	always "main"
design	Either "template" or "query" defining if template or query main effects are returned.
summary	If summary is "targets" the main effects are summarized per target gene.
QueryNr,TemplatePlate	Onle main effects of one query nr or one template plate are returned.
format	targetmatrix
withoutgroups	The genes within this group are not shown in the heatmap. It is convenient to hide screen controls.
do.inv.trafo	If TRUE, the data will be back-transformed for original scale of data. In the case of log-transformed data, the main effects are returned as factors, otherwise the main effects are returned as log values.
screen	The screen from which the main effects should be returned.
channel	The channel from which the main effects should be returned.
drop	Does return a drop array dimensions, even if only one screen or one channel is selected.
normalized	If true the normalized main effects are returned.

Value

An array containing the main effects.

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

data("sgi")
getMain(sgi)
getMainNeg(sgi)

RNAinteract documentation built on Nov. 8, 2020, 5:28 p.m.