makeCellHTS {imageHTS} | R Documentation

## 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.

### 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, gregoire.pau@embl.de, 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)

[Package imageHTS version 1.40.0 Index]