summarizeWells: Summarize cell features
In imageHTS: Analysis of high-throughput microscopy-based screens

Description Usage Arguments Details Value Author(s) See Also Examples

Compute phenotypic profiles by summarizing cell population features.

1	summarizeWells(x, uname, featurePar, profileFilename="data/profiles.tab", access='cache')

`x`	An imageHTS object.
`uname`	A character vector, containing the well names to summarize. See `getUnames` for details.
`featurePar`	A character string, indicating the filename containing the feature extraction parameters.
`profileFilename`	A character string, indicating the output filename to store the phenortpic profiles.
`access`	A character string indicating how to access the data. Valid values are `local`, `server` and `cache`, the default. See `fileHTS` for details.

summarizeWells computes for each well, summary statistics about cell features. Currently, cell number n and median cell feature med.* (for each feature) are computed.

Moreover, if the DCF segmentation parameters file pointed by featurePar includes the field cell.classes, containing a list of comma-separated cell classes, cell classes ratio are computed and included in the phenotypic profiles.

summarizeWells creates the file data/profiles.tab which contains the phenotypic profiles. Use readHTS to read this file.

A data frame, containing the phenotypic profiles.

Gregoire Pau, gregoire.pau@embl.de, 2010

extractFeatures, readHTS

  ## Not run: 
    ## initialize imageHTS object using the local submorph screen
    local = tempdir()
    server = system.file('submorph', package='imageHTS')
    x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
    x = configure(x, 'conf/description.txt', 'conf/plateconf.txt', 'conf/screenlog.txt')
    
    ## segment non-empty wells
    unames = setdiff(getUnames(x), getUnames(x, content='empty'))
    segmentWells(x, uname=unames, segmentationPar='conf/segmentationpar.txt')
    
    ## extract features
    extractFeatures(x, uname=unames, 'conf/featurepar.txt')
    
    ## cell classification
    readLearnTS(x, 'conf/featurepar.txt', 'conf/trainingset.txt')
    predictCellLabels(x, unames)
    
    ## summarize features
    summarizeWells(x, unames, 'conf/featurepar.txt')
    
    ## get profiles
    profiles = readHTS(x, type='file', filename='data/profiles.tab', format='tab')
  
## End(Not run)