getReplicateData: Extract replicates measurements from the screen.

In RNAinteract: Estimate Pairwise Interactions from multidimensional features

Description

A genetic interaction screen can contain within screen replicates, if some reagent pairs are measured at least twice. Usually this appears when measuring reagent pairs once as template-query and once as query-template. getReplicateData returns a list of these technical replicates.

If multiple reagents are used to target the same gene, different reagent pairs that target the same gene pair are extracted from the screen. These pairs are returned by getIndDesignData.

Usage

getReplicateData(sgi, screen, channel,
                 type = "data", design = "template",
                 do.trafo = TRUE, do.inv.trafo = FALSE,
                 normalized = FALSE)
getIndDesignData(sgi, screen, channel,
                 type = "data", design = "template",
		 do.trafo = TRUE, do.inv.trafo = FALSE,
		 normalized = FALSE)

Arguments

sgi	An object of class RNAinteract.
screen	The screen name from which the replicates will be extracted.
channel	The channel name from which the replicates will be extracted.
type	The type of data that is extracted. It is the type argument of the getData function.
design, do.trafo, do.inv.trafo, normalized	See the getData documentation for details.

Value

Returns a data.frame with columns x and y.

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

data("sgi")
res <- getIndDesignData(sgi, screen="1", channel="nrCells", type = "data")
plot(res$x, res$y)

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