imageHTS (version 1.22.0)

makeCellHTS: Segmentation of yeast cells and ring-shaped objects.

Description

makeCellHTS creates a cellHTS2 object.

Usage

makeCellHTS(x, profiles, measurementNames, name)

Arguments

x

An imageHTS object.

profiles

A data frame containing the phenotypic profiles. See Details.

measurementNames

An optional character vector containing the measurement names. If missing, column names of profiles are used.

name

An optional character string containing the name of the assay.

Value

Returns a cellHTS2 object.

Details

profiles is a data frame containing the phenotypic profiles, usually returned by summarizeWells or readHTS. Since cellHTS2 cannot handle large report, the dimension of the profiles must be lower than 10. This is usually done by subsetting columns or by dimension reduction.

See Also

summarizeWells, installWebQuery

Examples

 ## Not run: 
#    ## initialize kimorph object
#    localPath = file.path(tempdir(), 'kimorph')
#    serverURL = 'http://www.ebi.ac.uk/huber-srv/cellmorph/kimorph/'
#    x = parseImageConf('conf/imageconf.txt', localPath=localPath, serverURL=serverURL)
#    x = configure(x, 'conf/description.txt', 'conf/plateconf.txt', 'conf/screenlog.txt')
#    x = annotate(x, 'conf/annotation.txt')
#    
#    ## get profiles
#    profiles = readHTS(x, type='file', filename='data/profiles.tab', format='tab')
# 
#    ## prepare cellHTS2 report
#    ft = c('med.c.t.m.int', 'med.c.g.ss', 'med.c.g.ec', 'med.n.h.m.int', 'med.c.a.m.int')
#    measurementNames = c('tubulin intensity', 'cell size', 'cell eccentricity', 'dna intensity', 'actin intensity')
#    y = makeCellHTS(x, profiles[,c('uname', ft)], measurementNames=measurementNames, name='kimorph')
#    pathConf = file.path(localPath, 'conf')
#    y = configure(y, 'description.txt', 'plateconf.txt', 'screenlog.txt', path=pathConf)
#    y = annotate(y, 'annotation.txt', path=pathConf)
#    yn = normalizePlates(y, scale='multiplicative', log=FALSE,
#    method='median', varianceAdjust='none')
# 
#    ## write cellHTS2 report
#    se = getSettings()
#    se$plateList$intensities$include = TRUE
#    setSettings(se)
#    writeReport(raw=y, normalized=yn, outdir='report-cellHTS2', force=TRUE)
#   ## End(Not run)