qaProcess.marginevents {flowQ} | R Documentation |
This function takes a flowSet
as input and
creates all necessary output for a 'marginevents' type QA
process. Objects created by this function can be laid out as HTML
using writeQAReport
.
qaProcess.marginevents(set, channels=NULL, grouping=NULL, outdir, cFactor=2, absolute.value=NULL, name="margin events", sum.dimensions=NULL, det.dimensions=c(7,3), pdf=TRUE, ...)
set |
A flowSet . |
channels |
A character vector of channel names for which margin
events are to be recorded. Will use all available channels except
for the time channel if NULL . |
grouping |
A character vector defining one of the variables in
the phenoData of set used as a grouping variable. If this
argument is used and if absolute.value is NULL , outlier
detection will be performed within groups rather than across all
samples. |
outdir |
The directory to which the graphical output is to be saved. If multiple QA processes are to be combined, make sure to use the same directory for all of them. |
cFactor |
The outlier threshold at which the QA criterion is considered to have failed. This is essentially the factor of standard deviations away from the average number of cells per sample for the respective channel. |
absolute.value |
An absolute percentage of margin events below
which the QA criterion is considered to be failed. If this argument
is not NULL , cFactor is ignored. |
name |
The name of the process used for the headings in the HTML output. |
sum.dimensions, det.dimensions |
The dimensions of the pdf deviced in inches used for the summary plot and the sample-specific plots, respectively. |
pdf |
Logical indicating whether to create vectorized versions
of images for this quality process. This should be set to
FALSE if disk space is critical, since the pdf versions of
the image consume much more space on the hard drive compared to the
bitmap version. Setting the argument to FALSE will also
speed up the process. |
... |
Further arguments. |
QA processes of type 'marginevents' record the number of events that
fall on the margins of the measurement range for each
channel. Unproportionally high numbers of such events can indicate
problems with the instrument settings or with compensation. These are
either determined dynamically as outliers from the typical
distribution of margin event percentages for the whole set, or, if
absolute.value
is not NULL
, by an absolute cutoff
value. If there is a natural grouping among the samples, this can be
specified using the grouping
argument. In this case, the
outlier detection will be performed within its respective group for a
particular sample.
For more details on how to layout qaProcess
objects to
HTML, see writeQAReport
and qaReport
.
An object of class qaProcess
.
Florian Hahne
writeQAReport
, qaReport
,
qaProcess
, qaProcess.timeline
,
qaProcess.timeflow
, qaProcess.cellnumber
## Not run: data(GvHD) dest <- tempdir() qp <- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"), outdir=dest) qp ## End(Not run)