generateDatasetFile {RNAither} | R Documentation |
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)