MAPK.estimate.TPS: genetic interaction surfaces

In Huber-group-EMBL/RNAinteractMAPK: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi

Description

Genetic interaction surfaces are estimated from a dilution experiment. Cells are treated with two RNAi's. The concentration of the RNAi reagent is changed in 8 steps. All 8 x 8 combinations of concentrations are tested for 6 x 6 gene pairs.

Usage

MAPK.screen.as.array(data, Anno)
MAPK.estimate.TPS   (A, DF, n.out = 8, channel = 1)
MAPK.cv.TPS         (A, range.df = 6:56, channel = 1)
MAPK.plot.TPS.all   (TPSmodel, range = c(-6, 6), fill = c("cornflowerblue",
                     "cornflowerblue", "black", "#777700", "yellow"),
		     channel = 1)
MAPK.plot.TPS.single(gene1, gene2, TPSmodel, range = c(-6, 6),
                     fill = c("cornflowerblue", "cornflowerblue", "black",
		     "#777700", "yellow"), channel = 1)

Arguments

data, Anno

data	A data.frame containing the read.out of the dilution screen. Each row is one well. Each column one feature.
Anno	A data.frame containing the plate configuration. For each row in data there should a row in Anno.
A	An array of dimension concentration x concentration x genes x genes x channel as returned by MAPK.screen.as.array.
DF	A 6 x 6 matrix of degrees of freedom for the thin spline plate regression.
n.out	number of points for sampling from the regression function.
channel	The channel used.
range.df	The range of degrees of freedom that is considered for cross validation.
range	The range of pairwise interaction scores that is shown by the colorbar.
gene1, gene2	The genes for which the interaction surface is plotted.
TPSmodel	The TPS model estimated by MAPK.estimate.TPS
fill	The range of colors used for the color code.

Details

The screen readout can be reshaped as an array with dimensions concentration x concentration x genes x genes x channel by the function MAPK.screen.as.array. Then the function MAPK.estimate.TPS fits a regression in the 8 x 8 pairwise dilution series. The degrees of freedom for the regression can be estimated automatically by cross validation with the function MAPK.cv.TPS. Finally one can plot the interaction surface for a single gene or an overview of interaction surfaces for all genes with the functions MAPK.plot.TPS.single or MAPK.plot.TPS.all.

Value

• MAPK.screen.as.array returns an array of dimensions concentration x concentration x genes x genes x channel with the screen data.

• MAPK.estimate.TPS returns a regression model estimated by thin plate splines for each pair of genes and subsampled matrices.

• MAPK.cv.TPS.all returns

  • DF a matrix with degrees of freedom.

  • CVerror The prediction error estimated by cross validation.

  • CVerrorSD The standard deviation of the prediction error estimated by cross validation.

• MAPK.plot.TPS.single,MAPK.plot.TPS.all: An object of class "trellis". See levelplot for details.

Author(s)

Bernd Fischer

See Also

RNAinteract-package, RNAinteractMAPK-package

Huber-group-EMBL/RNAinteractMAPK documentation built on Dec. 31, 2020, 1:01 p.m.