Create a matrix with replicate data in columns

Description

Given an array of raw or normalized intensities (xraw or xnorm) of a cellHTS object, creates a matrix with the data from the chosen channel.

Usage

getMatrix(y, channel=1, na.rm=FALSE)

Arguments

Details

Given as input an array y (e.g., the slot xraw, or xnorm of a cellHTS object) with dimensions nr wells x nr plates x nr replicates x nr channels, this function creates a matrix with the data for the chosen channel. Each replicate corresponds to a column of the output matrix. If na.rm is set to TRUE, only the positions with available values for all the replicates are given in the output matrix.

Value

A matrix with the same number of columns as the number of replicates (third dimension of y). If na.rm=FALSE (the default), the number of rows of the output matrix is identical to the product between the first two dimensions of y (nr wells x nr plates). If na.rm=TRUE, only the rows with no missing entries in all the replicates (columns) are given.

Author(s)

Ligia Bras ligia@ebi.ac.uk

Examples

    data(KcViabSmall)
    y <- getMatrix(KcViabSmall$xraw)

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)

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> library(cellHTS)
Loading required package: grid
Warning message:
Package 'cellHTS' is deprecated and will be removed from Bioconductor
  version 3.4. Please consider using 'cellHTS2' which offers better
  functionality for working with multiple screens and with
  multi-channel screens. 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS/getMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getMatrix
> ### Title: Create a matrix with replicate data in columns
> ### Aliases: getMatrix
> ### Keywords: manip
> 
> ### ** Examples
> 
>     data(KcViabSmall)
>     y <- getMatrix(KcViabSmall$xraw)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>