RNAither (version 2.20.0)

generateDatasetFile: Generate Dataset File

Description

Generates a text file containing all experimental data. Needed for all subsequent analysis functions.

Usage

generateDatasetFile(externalExperimentName, typeOfData, comments, outputFile, 
plateLayoutInternal, plateLayoutNCBI, nbRowsPerPlate, nbColsPerPlate, screenNb_pre, 
emptyWells, poorWells, controlCoordsOutput, backgroundValOutput, meanSignalOutput, 
SDmeanSignal, objNumOutput, cellNumOutput)

Arguments

externalExperimentName

A character string specifying the experiment name, e.g. "Johns Experiment Nb. 1"

typeOfData

A character string specifying the type of data, e.g. "364 well plate data for virus screens"

comments

A character string specifying comments. NA if not available.

outputFile

A character string specifying the name of the text file containing the dataset.

plateLayoutInternal

A matrix of internal siRNA IDs specifying their position on the plate (row-wise). Each column of the matrix stands for one plate.

plateLayoutNCBI

A matrix of gene names specifying their position on the plate (row-wise). Each column of the matrix stands for one plate.

nbRowsPerPlate

The number of rows per plate

nbColsPerPlate

The number of columns per plate

screenNb_pre

The screen/experiment number

emptyWells

A list containing, for each plate, an integer vector of the positions of empty wells. NA if there are no empty wells on the plate.

poorWells

A list containing, for each plate, an integer vector of the positions of wells that, for a certain reason, should not be taken into account during the analysis. NA if there are no such wells on the plate.

controlCoordsOutput

A list containing, for each plate, a list of integer vectors specifying the positions of positive (first element in sublist) and negative (second element in sublist) controls. NA if there are no positive/negative controls on the plate.

backgroundValOutput

A list containing, for each plate, a vector of background values per well

meanSignalOutput

A list containing, for each plate, a vector of intensity values for each well

SDmeanSignal

A list containing, for each plate, a vector of standard deviations of intensity values for each well

objNumOutput

A list containing, for each plate, a vector of the number of identified objects for each well

cellNumOutput

A list containing, for each plate, a vector of intensity values for each well, e.g. a vector of the number of identified cells for each well.

Value

The function generates a text file consisting of a header and a 'dataset'. The header contains the experiment description (ExternalExperimentName, TypeOfData and Comments). The dataset is an R data frame, each row corresponding to one well, with the following columns:

Spotnumber

The position of the well on the plate

Internal_GeneID

The ID of the siRNA

GeneName

The gene name

SpotType

Can be -1, 0, 1 or 2.Type -1 wells (e.g. emtpy wells, wells with poor quality) are not considered in subsequent analyses but are kept in the data set for the sake of completeness.Type 0 wells correspond to negative controls, type 1 wells to positive controls.Type 2 wells correspond to the standard data wells.

SigIntensity

The signal intensity (channel 1)

SDSIntensity

The standard deviation of the signal intensity, if available

Background

The background per well, if available

LabtekNb

The plate number

RowNb

The row number

ColNb

The column number

ScreenNb

The screen number

NbCells

E.g. the number of cells identified in the well (channel 2)

PercCells

The ratio (number of identified cells)/(number of identified objects)

Details

Positions on plates are specified with one integer only. For example, the position of the well in row 2 and column 5 is (RowNo-1)*(Number of columns on plate)+ColNo.

See Also

joinDatasetFiles, joinDatasets

Examples

##gene names
plateLayout1 <- c("test1", "empty", "test3", "test4", "test5", 
"test6", "test7", "empty", "test9", "test10", "test11", "test12")

plateLayout2 <- c("test1", "test2", "test3", "test4", "test5", 
"test6", "test7", "test8", "test9", "test10", "test11", "test12")

plateLayout <- cbind(plateLayout1, plateLayout2)

emptyWells <- list(c(2, 8), NA_integer_)
##the first plate has two empty wells at position 2 and 8,
##the second plate does not have any empty wells

poorWells <- NA_integer_
##no wells of poor quality

controlCoordsOutput <- list(list(NA_integer_, NA_integer_), list(NA_integer_, c(9,10)))
##the first plate does not have any control siRNAs,
##the second plate has two negative controls at position 9 and 10

backgroundValOutput<-NA_integer_
##no background signal intensities available

sigPlate1<-c(2578, NA_integer_, 3784, 3784, 2578, 5555, 5555, NA_integer_, 8154, 2578, 3784, 2578)
sigPlate2<-c(8154, 3784, 5555, 3784, 11969, 2578, 1196, 5555, 17568, 2578, 5555, 2578)
##the signal intensities on the plates

meanSignalOutput<-list(sigPlate1, sigPlate2)

SDmeansignal<-NA_integer_
##no standard deviation available

objnumOutput<-NA_integer_
##no cell count available

cellnumOutput<-NA_integer_

generateDatasetFile("First test screen", "RNAi in virus-infected cells", 
NA_character_, "testscreen_output.txt", plateLayout, plateLayout, 3, 4, 
1, emptyWells, poorWells, controlCoordsOutput, backgroundValOutput, 
meanSignalOutput, SDmeansignal, objnumOutput, cellnumOutput)

##load the dataset into R:
header<-readLines("testscreen_output.txt",3)
dataset<-read.table("testscreen_output.txt", skip=3, colClasses=c(NA, NA, NA, NA, 
"factor", NA, NA, NA, NA, NA, NA, NA, NA, NA), stringsAsFactors=FALSE)