RNAinteract (version 1.20.0)

getMain: get main effects

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.

See Also

RNAinteract-package

Examples

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