Last data update: 2014.03.03

R: Primary access function for all screen data.
getDataR Documentation

Primary access function for all screen data.

Description

This function is the primary access function for a wide range of data from the screen. It does perform normalization, transformation, and reshaping if specified.

Usage

getData(sgi, type = "data", format = "plain",
	design = "template", mixTemplateQuery = TRUE,
	screen = NULL, channel = NULL,
	do.trafo = TRUE, do.inv.trafo = FALSE,
	normalized = FALSE, withoutgroups = c(),
	drop = TRUE)

Arguments

sgi

An object of class RNAinteract

type

Specifies which data is returned. Possible values are:

  • "p.value", "q.value": returns the p-value or q-value as computed by computePValues.

  • "data": returns the input data.

  • "pi": returns the pairwise interaction score.

  • "plateeffect": returns the plate effect estimated by normalizePlateEffect.

  • "ni.model" returns the non-interacting model as estimated by estimateMainEffect.

  • "main": returns the main effects.

  • "mainsderr": returns the std error of the main effects.

  • "mainsd": returns the std deviation of the main effects.

  • "maintime": returns the estimated time effect as estimated by normalizeMainEffectQuery

  • "mainspatial": returns the estimated spatial effect as estimated by normalizePlateEffect

format

The output format. Possible values:

  • "plain": The data can be returned as a plain vector

  • "platelist": a list of plate matrices that can be passed to plotScreen

  • "reagentMatrix": All values for the same reagent pair are summarized in a matrix of dimension reagents x reagents

  • "targetMatrix": All values for the same gene pair are summarized in a matrix of dimension genes x genes

design

If type is one of the main effect types, the design can be specified to state if the "template" or "query" main effect is returned.

mixTemplateQuery

If TRUE, The template-query and query-template entries in the matrix are symmetrized.

screen

The screen names of which data should be returned.

channel

The channel names of which data should be returned.

do.trafo

Only effective, if type is "data". If TRUE, the data is transformed.

do.inv.trafo

Not effective if type is "data", "p.value", or "q.value". If TRUE, the values are back-transformed to the original scale.

normalized

If TRUE, the normalization data is returned.

withoutgroups

The genes from the specified groups are not returned in the data.

drop

If FALSE, the returned array is reduced in dimensions, whenever there is a dimension 1.

Value

An array containing the specified values is returned. In the case, the format is chosen to be "platelist", a list of matrices is returned.

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

data("sgi")

# get the original data, as plain file, reshaped in plate layout,
# reshaped and summarized as target matrix
D <- getData(sgi, type="data", do.inv.trafo = TRUE)
Dplatelayout <- getData(sgi, type="data", 
	     format="platelist", do.inv.trafo = TRUE)
splots::plotScreen(Dplatelayout[["1"]][["nrCells"]],
	     nx=sgi@pdim[2], ny=sgi@pdim[1], ncol=3)
Dmatrix <- getData(sgi, type="data", 
	     format="targetMatrix", do.inv.trafo = TRUE)

# get main effects as plate layout with specified transformation
# (usually log-transformed)
Mplatelayout <- getData(sgi, type="main", design="template", 
	     screen="1", channel="nrCells", format="platelist")
splots::plotScreen(Mplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1],
	     ncol=3)

# get non-interacting model and pairwise interaction scores as matrix
NImatrix <- getData(sgi, type="ni.model", format="targetMatrix")
PImatrix <- getData(sgi, type="pi", format="targetMatrix")
PIplatelayout <- getData(sgi, type="main", design="query",
	     screen="1", channel="nrCells", format="platelist")
splots::plotScreen(PIplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1],
             ncol=3)

# get p-values and q-values
PVmatrix <- getData(sgi, type="p.value", format="targetMatrix")
QVmatrix <- getData(sgi, type="q.value", format="targetMatrix")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/getData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getData
> ### Title: Primary access function for all screen data.
> ### Aliases: getData
> ### Keywords: attribute
> 
> ### ** Examples
> 
> data("sgi")
> 
> # get the original data, as plain file, reshaped in plate layout,
> # reshaped and summarized as target matrix
> D <- getData(sgi, type="data", do.inv.trafo = TRUE)
> Dplatelayout <- getData(sgi, type="data", 
+ 	     format="platelist", do.inv.trafo = TRUE)
> splots::plotScreen(Dplatelayout[["1"]][["nrCells"]],
+ 	     nx=sgi@pdim[2], ny=sgi@pdim[1], ncol=3)
> Dmatrix <- getData(sgi, type="data", 
+ 	     format="targetMatrix", do.inv.trafo = TRUE)
> 
> # get main effects as plate layout with specified transformation
> # (usually log-transformed)
> Mplatelayout <- getData(sgi, type="main", design="template", 
+ 	     screen="1", channel="nrCells", format="platelist")
> splots::plotScreen(Mplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1],
+ 	     ncol=3)
> 
> # get non-interacting model and pairwise interaction scores as matrix
> NImatrix <- getData(sgi, type="ni.model", format="targetMatrix")
> PImatrix <- getData(sgi, type="pi", format="targetMatrix")
> PIplatelayout <- getData(sgi, type="main", design="query",
+ 	     screen="1", channel="nrCells", format="platelist")
> splots::plotScreen(PIplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1],
+              ncol=3)
> 
> # get p-values and q-values
> PVmatrix <- getData(sgi, type="p.value", format="targetMatrix")
> QVmatrix <- getData(sgi, type="q.value", format="targetMatrix")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>