generateDatasetFile: Generate Dataset File
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Details Value See Also Examples

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

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

`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.

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.

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)

joinDatasetFiles, joinDatasets

##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)