Name 
Type 
Default 
Description 
IDCol 
string 
""

The column representing the row numbers. The parameter is optional and it would be added to the
"postProb" files, if provided. 
NaRmove 
boolean 
true

Whether remove the rows with na from the data or return an Error. 
channelsToCluster 
string 
(no default)

A commaseparated list of column names or column numbers (e.g. channel names/
numbers in flow cytometry analysis), to be clustered. As for instance the value
could be set as "1, 2, 3, 4, 5" or "FSC.A, SSC, ERK1, STAT1, CD4" . 
channelsToRegularPlot 
string 
""

A commaseparated list of column names or column numbers (e.g. channel names/
numbers in flow cytometry analysis), to be plotted. As for instance the value
could be set as "1, 2, 3, 4, 5" or "FSC.A, SSC, ERK1, STAT1, CD4". This parameter is only for the "regular2d" and "regullar3d" plottings. 
clusterIDColName 
string 
"cluster"

The name of the column in the clusters output
which contains the cluster IDs of the rows. 
density 
string 
"skewt"

Density distribution to be used for clustering: normal, t, skew
normal, skew t. 
epsilon 
float 
0.0001

A value used for threshold in the mixture modeling fitting process. The
smaller the value the more accurate the cluster results are. If the clusters do
not satisfy the epsilon threshold in iterationMaximum iteration attempts an
error would be returned. 
estimateMode 
boolean 
false

Used only for skew distributions. Whether to estimate the mode
for each cluster. The defalt value (i.e. false) is recommended 
gMax 
int 
5

The maximum number of the "Mixture Model" clusters. It is considering that
results for some clusters might be Null. As for instance, the results for
MMclustering with g parameter (i.e. expected cluster number) of 5 might group the
rows of the data in 4 clusters of 1,2,4,and 5. 
gMin 
int 
3

The minimum number of the Mixture Model clusters.It is considering that
results for some clusters might be Null. As for instance, the results for
MMclustering with g parameter (i.e. expected cluster number) of 5 might group the
rows of the data in 4 clusters of 1,2,4,and 5. 
includePosterior 
boolean 
true

Whether include the Posterior probabilities. Check "the postProb" output for more information. 
iterationMaximum 
int 
5000

The maximum limitation for the number of iterations, in the mixturemodeling fitting process 
nSlaves 
int 
5

The number of the clusters used for paralelising the Mixture
Modeling. 
pagebreak 
boolean 
false

Tells if the result document should start with a page break. 
pch 
string 
"."

The type and shape of plotting points. Numbers (e.g. "2") and characters (e.g. ".") are possible. 
plotType 
string 
"boundry2d"

The type of Plotting. The choices are regular2d, regular3d,
contour2d, individualcontour2d, and boundry2d. 
randomSeed 
int 
1984

The seed value for semirandom processes 
step 
float 
0.5

Only used when Density is "skew" and the estimateMode is "true".
It is used to calculated the number of the iterations of the
ExpectedMaximization (i.e. EM), while computing the Maximum
Likelihood (i.e ML) estimate. The value should be greater than 0.
The smaller the value, the more accurate the estimations would be. 
writeImage 
boolean 
false

Whether include the plotting images in the report directory. 
writeParams 
boolean 
false

Whether write the Mixture Model parameters. 