summarizeWells {imageHTS} | R Documentation |
Compute phenotypic profiles by summarizing cell population features.
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 |
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 |
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
## 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)