Description Usage Arguments Value Author(s) Examples
For a set of FCS files, flow_auto_qc performs a complete and automatic quality control. It consists in the detection and removal of anomalies by checking three properties of flow cytometry: 1) flow rate, 2) signal acquisition, 3) dynamic range.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | flow_auto_qc(
fcsfiles,
remove_from = "all",
output = 1,
timeCh = NULL,
second_fractionFR = 0.1,
alphaFR = 0.01,
decompFR = TRUE,
ChExcludeFS = c("FSC", "SSC"),
outlier_binsFS = FALSE,
pen_valueFS = 500,
max_cptFS = 3,
ChExcludeFM = c("FSC", "SSC"),
sideFM = "both",
neg_valuesFM = 1,
html_report = "_QC",
mini_report = "QCmini",
fcs_QC = "_QC",
fcs_highQ = FALSE,
fcs_lowQ = FALSE,
folder_results = "resultsQC"
)
|
fcsfiles |
It can be a character vector with the filenames of the FCS files, a flowSet or a flowFrame. |
remove_from |
Select from which of the three steps the anomalies have to
be excluded in the high quality FCS file. The default option |
output |
Set it to 1 to return a flowFrame or a flowSet with high
quality events only. Set it to 2 to return a flowFrame or a flowSet with an
additional parameter where the low quality events have a value higher than
10,000. Set it to 3 to return a list with the IDs of low quality cells.
Set it to any other value if no R object has to be returned. Default is
|
timeCh |
Character string corresponding to the name of the Time Channel
in the set of FCS files. By default is |
second_fractionFR |
The fraction of a second that is used to split the
time channel in order to recreate the flow rate. Set it to
|
alphaFR |
The level of statistical significance used to accept anomalies
detected by the ESD method. The default value is |
decompFR |
Logical indicating whether the flow rate should be decomposed
in the trend and cyclical components. Default is |
ChExcludeFS |
Character vector with the names or name patterns of the
channels that you want to exclude from the signal acquisition check. The
default option, |
outlier_binsFS |
logical indicating whether outlier bins (not events)
have to be removed before the changepoint detection of the signal
acquisition check. The default is |
pen_valueFS |
The value of the penalty for the changepoint detection
algorithm. This can be a numeric value or text giving the formula to use;
for instance, you can use the character string |
max_cptFS |
The maximum number of changepoints that can be detected for
each channel. The default is |
ChExcludeFM |
Character vector with the names or name patterns of the
channels that you want to exclude from the signal acquisition check. The
default option, |
sideFM |
Select whether the dynamic range check has to be executed on
both limits, the upper limit or the lower limit. Use one of the options:
|
neg_valuesFM |
Scalar indicating the method to use for the removal of
the anomalies from the lower limit of the dynamic range. Use |
html_report |
Suffix to be added to the FCS filename to name the HTML
report of the quality control. The default is |
mini_report |
Name for the TXT file containing the percentage of
anomalies detected in the set of FCS files analyzed. The default is
|
fcs_QC |
Suffix to be added for the filename of the new FCS containing a
new parameter where the low quality events only have a value higher than
10,000. The default is |
fcs_highQ |
Suffix to be added for the filename of the new FCS
containing only the events that passed the quality control. The default is
|
fcs_lowQ |
Suffix to be added for the filename of the new FCS containing
only the events that did not pass the quality control. The default is
|
folder_results |
Character string used to name the directory that
contains the results. The default is |
A complete quality control is performed on flow cytometry data in FCS format. By default the analysis returns:
1. a flowFrame or flowSet object containing new FCS files with only high quality events
and a directory named resultsQC containing:
1. a set of new FCS files with a new parameter to gate out the low quality events a value larger than 10,000 is assigned to them only,
2. a set of HTML reports, one for each FCS file, that include graphs and table indicating where the anomalies were detected,
3. a single TXT file reporting the percentage of events removed in each FCS file.
Gianni Monaco, Chen Hao
1 2 3 4 5 |
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