getMatrix: Create a matrix with replicate data in columns

In cellHTS: Analysis of cell-based screens

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

y	an array with four dimensions, such as the slot xraw or xnorm of a cellHTS object.
channel	a numeric value corresponding to the selected channel of y. By default, the first channel (that is, y[,,,1] is considered).
na.rm	Logical, indicated if the missing values should be omitted.

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 [e-mail]

Examples

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

cellHTS documentation built on Oct. 5, 2016, 4:40 a.m.