summarizeWells {imageHTS} | R Documentation

## Summarize cell features

### Description

Compute phenotypic profiles by summarizing cell population features.

### Usage

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

### Arguments

`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.

### 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.

### Value

A data frame, containing the phenotypic profiles.

### Author(s)

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

### See Also

`extractFeatures`, `readHTS`

### Examples

      ## 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)

[Package imageHTS version 1.34.0 Index]