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Last data update: 2014.03.03

R: Extract replicates measurements from the screen.

getReplicateData

R Documentation

Extract replicates measurements from the screen.

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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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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/getReplicateData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getReplicateData
> ### Title: Extract replicates measurements from the screen.
> ### Aliases: getReplicateData getIndDesignData
> ### Keywords: attribute
> 
> ### ** Examples
> 
> data("sgi")
> res <- getIndDesignData(sgi, screen="1", channel="nrCells", type = "data")
> plot(res$x, res$y)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>