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

In imageHTS: Analysis of high-throughput microscopy-based screens

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.

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.

Value

Returns a cellHTS2 object.

Author(s)

Gregoire Pau, [e-mail], 2010

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)

imageHTS documentation built on Nov. 8, 2020, 8:29 p.m.