Keywords

This section lists and describes the keywords that are created by ModFit LT. These keywords can be selected for display on reports using the Keywords command in the Tools menu, and can be stored in a database as well.

Some keywords are available only when the conditions they relate to exist. For example, keywords related to a second DNA Aneuploid population will only be available if the model that is used contains components for a second Aneuploid cycle.

NOTE: The keywords for second, third, and fourth aneuploid cycles are identical to those for the first, except that they are prefixed with Z_An2, Z_An3, and Z_An4 instead of Z_An1.

Standard Model Keywords	Comment
Z_Aggregates	% aggregates
Z_AllCycleEvents	Sum of events in cycles
Z_An1	% events in first aneuploid cycle
Z_An1_BAD	% BAD in first aneuploid cycle
Z_An1_CV	% CV for first aneuploid cycle G1
Z_An1_DI	DNA index of G1 in first aneuploid cycle
Z_An1_G1	% of first aneuploid cycle in G1
Z_An1_G1_Mean	Mean of G1 in first aneuploid cycle
Z_An1_G2	% of first aneuploid cycle in G2
Z_An1_G2_Mean	Mean of G2 in first aneuploid cycle
Z_An1_G2G1Ratio	G2/G1 ratio for first aneuploid cycle
Z_An1_Ploidy	Ploidy of first aneuploid cycle
Z_An1_S	% of first aneuploid cycle in S-Phase
Z_AneuploidS_Bnd	S-Phase assessment cut-off value
Z_AneuploidS_Class	S-Phase assessment classification
Z_AneuploidS_PValue	S-Phase P-value
Z_AneuploidS_Std	S-Phase assessment standard deviation
Z_CycleEventsPerChannel	Average number of events per channel in cycles.
Z_Debris	% debris
Z_Dip	% events in diploid cycle
Z_Dip_BAD	% BAD in diploid cycle
Z_Dip_CV	% CV for diploid cycle G1
Z_Dip_G1	% of diploid cycle in G1
Z_Dip_G1_Mean	Mean of G1 in diploid cycle
Z_Dip_G2	% of diploid cycle in G2
Z_Dip_G2_Mean	Mean of G2 in diploid cycle
Z_Dip_G2G1Ratio	G2/G1 ratio for diploid cycle
Z_Dip_Ploidy	Ploidy of diploid cycle
Z_Dip_S	% of diploid cycle in S-Phase
Z_DiploidS_Bnd	S-Phase assessment cut-off value
Z_DiploidS_Class	S-Phase assessment classification
Z_DiploidS_PValue	S-Phase P-value
Z_DiploidS_Std	S-Phase assessment standard deviation
Z_LinearityFactor	Linearity value used in the model
Z_MAE	Mean Absolute Error For details, see https://en.wikipedia.org/wiki/Mean_absolute_error
Z_ModeledEvents	Number of events accounted for by the model
Z_nRCS	Normalized RCS value, which is the RCS computed on the area normalized to 10,000 events.
Z_PloidyStatus	S-Phase assessment ploidy
Z_RCS	Reduced chi-square
Z_RMSD	Root Mean Square Deviation. For details, see https://en.wikipedia.org/wiki/Root-mean-square_deviation
Z_Stnd1	% of events in first internal standard
Z_Stnd1_DI	DNA Index of first standard
Z_Stnd1_DipG1Ratio	DipG1 mean/First Std mean
Z_Stnd1_Mean	Mean of first standard
Z_Stnd2	% of events in second internal standard
Z_Stnd2_DI	DNA Index of second standard
Z_Stnd2_DipG1Ratio	DipG1 mean/Second Std mean
Z_Stnd2_Mean	Mean of second standard
Z_TotalAneuploidFraction	Percentage of cells in aneuploid cycles
Z_TotalAneuploidS	(Sum all aneuploid S-Phase areas)*100/(Sum all aneuploid areas). For simple Diploid models, the keyword reports the value of Diploid S-Phase. You may think of this keyword as "tumor S-Phase."
Z_TotalBAD	% BAD for histogram
Z_TotalS	Average or total S-Phase
Z_TotalS_Bnd	S-Phase assessment cut-off value
Z_TotalS_Class	S-Phase assessment classification
Z_TotalS_PValue	S-Phase P-value
Z_TotalS_Std	S-Phase assessment standard deviation

The following keywords store configuration values used by the program. The Auto Analysis Settings, Peak Finder Settings, and Options and Configuration dialog boxes set these values.

Configuration Keywords	Comment
CF_APOPTOSIS	Auto Analysis state for apoptosis
CF_AUTOAGGREGATE	Auto Analysis state for AutoAggregates
CF_AUTODEBRIS	Auto Analysis state for AutoDebris
CF_MOD_S_COMPARTMENTS	Number of S-Phase compartments in this model
CF_MOD_S_SHAPE	Shape of S-Phase in this model
CF_G2G1RATIO	Auto Analysis state for linearity or G2/G1 ratio
CF_PLOIDY_DIP_STD_RATIO	Auto Analysis state for diploid-to-standard ratio
CF_PLOIDY_MODE	Auto Analysis state for ploidy detection mode
CF_SPHASE_COMPARTMENTS	Auto Analysis state for number of S-Phase compartments
CF_SPHASE_SHAPE	Auto Analysis state for shape of S-Phase
CF_SPHASE_DI_THRESHOLD	Auto Analysis state for DI for S-Phase
CF_TET_RANGE	Auto Analysis state for Tetraploid range
CF_PF_STATE	State for Peak Finder
CF_PF_RISE	Peak Finder setting for rise
CF_PF_LOWCV	Peak Finder setting for low CV
CF_PF_HIGHCV	Peak Finder setting for high CV
CF_PF_CC	Peak Finder setting for correlation coefficient
CF_PF_PCNTSTART	Peak Finder setting for starting threshold

MF keywords

Internal keywords are prefixed with "MF_" and store data computed by the program. They are listed in the table below.

Internal Keywords	Comment
MF_ANALYSIS	Type of analysis performed
MF_AUTODEBRIS_FIRSTCUT	Setting for AutoDebris first cut
MF_AUTODEBRIS_RESOLUTION	Setting for AutoDebris resolution
MF_AUTODEBRIS_SECONDCUT	Setting for AutoDebris second cut
MF_AUTODEBRIS_THIRDCUT	Setting for AutoDebris third cut
MF_DATE	Date of analysis
MF_FILE	Full path name of the data file
MF_FILEPATH	Pathway to the data file
MF_GATE1	Parameters for gate
MF_GATE1_PERCENT	Percent of events in gate
MF_GATE2	Parameters for gate
MF_GATE2_PERCENT	Percent of events in gate
MF_GATE3	Parameters for gate
MF_GATE3_PERCENT	Percent of events in gate
MF_MODEL	Name of the model used in analysis
MF_PLOIDYINDEX	0=Diploid, 1=Tetraploid, 2= One Aneuploid, 3=Two Aneuploid, etc.
MF_RCS	Reduced chi-square
MF_REPORT	Name of the report
MF_REPORTPATH	Pathway to the report
MF_TIME	Time of the analysis
MF_VERSION	Version of the program

USER keywords

These keywords show the results of user-entered equations found in Options and Configuration dialog. The name for the keyword is prefixed with "USER_". This allows you to display and database results of user-entered equations.

C keywords

Keywords that begin with "C_" display the final value for a detail of a model component. The naming convention starts with "C_", followed by the name of the component, an underscore, and the name of the detail. For example, "C_An1 G1_Area" displays the area of the An1 G1 component.

Sync Wizard keywords

When using the Sync Wizard, several additional keywords are made available. These allow you to extract the percentage of each compartment used in modeling S-Phase. If, for example, you use 3 rectangles to model S-Phase, you will find three additional keywords: Z_DIPS_C1, Z_DIPS_C2, Z_DIPS_C3.

Proliferation Wizard keywords

When using the Proliferation Wizard, additional keywords are available to allow you to display and database all of the information generated by the wizard. These keywords are prefixed with "Z_PROLIF", and are named to indicate the value that it stores.