generateDatasetFile {RNAither} | R Documentation

## 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.

### 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`.

### 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)

### 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)

[Package RNAither version 2.28.0 Index]