makeCellHTS {imageHTS} | R Documentation |
makeCellHTS
creates a cellHTS2 object.
makeCellHTS(x, profiles, measurementNames, name)
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 |
name |
An optional character string containing the name of the assay. |
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.
Returns a cellHTS2
object.
Gregoire Pau, gregoire.pau@embl.de, 2010
summarizeWells
, installWebQuery
## Not run: ## initialize kimorph object localPath = file.path(tempdir(), 'kimorph') serverURL = 'http://www.huber.embl.de/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)