Creates a directory with HTML pages of linked tables and plots
documenting the contents of the preprocessing of a
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the intitial raw
a list of
a character of length 1 with the name of a directory
where to write the report HTML file and images. If the directory
does not exist, it is created. If it exists and is not empty, then
the behaviour depends on the value of
a logical value, determines the behaviour of the function
a logical value indicating whether tooltips with the
annotation should be added to the plate plots and image
screen. Default value is FALSE. NOTE: This argument is deprecated
and will go away in the next release. Please see
either a list with parameters for the plate plots
of the per plate quality report pages, or a logical scalar with
a list with parameters for the function
a list or vector of regular expressions specifying the name of the positive controls. See details.
a vector of regular expressions specifying the name of the negative controls. See details.
The path to the R script generating the current report. We strongly advice to store this script in the compendium for future reference.
Add the output of a gene set enrichment analysis to the report. This is totally experimental at this time.
A named list of settings controlling the output of
The function has to be called with the mandatory argument
corresponding to an unnormalized
optional arguments are:
cellHTS object containing
cellHTS object containing data scored
this component is available, then
should also be given.
All of the above arguments have to be
cellHTS objects containing
data from the same experiment, but in different preprocessing stages.
cellHTS argument is deprecated and should no be used anymore.
The following elements are recognized for
passed on to
sdcol, the color
scheme for the standard deviation plate plot,
sdrange, the sd
range to which the colors are mapped,
xcol, the color scheme for
the intensity plate plot,
xrange, the intensity range to which
the colors are mapped. If an element is not specified, default values
are used. Both
xrange can also be provided as
functions, which take the values to be plotted by
platePlot as a
single argument and has to return a numeric vector of length 2. See its
documentation for details.
The following elements are recognized for
passed on to
anno, gene annotation for the image
From now on, all settings controlling the output of
should either be provided through the
settings argument, or as
session-wide parameters set using
setSettings. Please see
settings for details.
negControls should be given as a vector of
regular expression patterns specifying the name of the positive(s) and
negative(s) controls, respectivey, as provided in the plate
configuration file (and acccessed via
cellHTS object containing normalized data was provided as argument
norm, the length of
negControls should be equal to the number of channels in this
dim(Data(cellHTSlist[["normalized"]]))). Otherwise, the
length of these vectors should be equal to the number of channels in the
cellHTS object (i.e.,
By default, if
posControls is not given, "pos" will be taken as
the name for the wells containing positive controls. Similarly, if
negControls is missing, by default "neg" will be considered as
the name used to annotate the negative controls. The content of
negControls will be passed to
regexpr for pattern matching within the well
annotation given in column
controlStatus of the
featureData slot of the
cellHTS object. If no controls are
available for a given channel, use
NA for that
channel. For example,
posControls = c("", "(?i)^diap$") means
that channel 1 has no positive controls, while "diap" is the positive
control for channel 2.
negControls are particularly
useful in multi-channel data since the controls might be
reporter-specific, or after normalizing multi-channel data.
In the case of a two-way assay, where two types of "positive" controls
are used in the screen ("activators" and "inhibitors"),
posControls should be defined as a list with two components
inh), each of which should be vectors of
regular expressions of the same length as the current number of
reporters (as explained above).
By default, tooltips doing the mapping between the probe annotation and
the plate wells are not added to the plate plots and to the overall
screen plot. If any of the
cellHTS objects in
is annotated, the probe annotation uses the information contained
either in column
GeneSymbol or column
GeneID (if the
former is missing) of the
featureData slot of the annotated
cellHTS object. Otherwise, the mapping simply uses the well
The function is called for its side-effect. It returns a character with the full path and name of the report index file, this is an HTML file which can be read by a web browser.
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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data(KcViabSmall) pCtrls <- c("pos") nCtrls <- c("neg") ## Not run: ## or for safety reasons (not a problem for the current well annotation, however) pCtrls <- c("^pos$") nCtrls <- c("^neg$") writeReport(raw=KcViabSmall, posControls=pCtrls, negControls=nCtrls) ## same as ## writeReport(raw=KcViabSmall) xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median") xsc <- scoreReplicates(xn, sign="-", method="zscore") xsc <- summarizeReplicates(xsc, summary="min") ## to turn on the tooltips in the plate plots and in the image screen plot: writeReport(raw=KcViabSmall, normalized=xn, scored=xsc, force=TRUE, map=TRUE, plotPlateArgs = TRUE, imageScreenArgs=list(zrange=c(-4,4))) ## End(Not run)