imageHTS (version 1.22.0)

summarizeWells: 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.

Value

A data frame, containing the phenotypic profiles.

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.

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)