createFluo: createFluo

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

The data format creator function for the signal normalization step.

Usage

createFluo(data, dateIndex = c(), from.file = FALSE, separator = "_")

Arguments

data	Data matrix. The output data matrix of LocationMatrix().
dateIndex	a date index to be used for storing the output files. It is either transfered from LocationMatrix() or it is generated here for the first time (e.g. if image analysis was not run by CONFESS or if the analysis has been repeated many times).
from.file	Logical. If TRUE the data is read from a file whose format should be the same to the output of LocationMatrix(). Default is FALSE.
separator	Character string. It separates the run ID from the Well ID in the image filenames (the <<separator1>> of readFiles()). It is also used here to enable the user perform the analysis independently of the previous step (cell recognition via imaging). Default is "_".

Value

A list of reformed data to be used in subsequent analysis: index: The sample indices. RGexprs: the foreground (columns 1 and 3) and background (columns 2 and 4) signals of each channel that have been estimated by spotEstimator() and filtered in LocationMatrix(). samples: the sample IDs. batch: a matrix of the run IDs. The first column contains the original run IDs. The second column is the converted original IDs into numeric values (to be used in the statistical modeling step of Fluo_adjustment()). size: the estimated cell size. image.type: the image type IDs as defined in readFiles(). The parameter is kept in ordeer to enable the user to use this function independently of the image analysis step. dateIndex: a date index to be used for storing the output files. It is either transfered from LocationMatrix() or it is generated here for the first time (e.g. if image analysis was not run by CONFESS or if the analysis has been repeated many times).

Examples

step1 <- createFluo(from.file=system.file("extdata", "Results_of_image_analysis.txt",
package = "CONFESS"),separator="_")

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.