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sample.cfg
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63 lines (51 loc) · 4 KB
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####################################################################################################
# #
# #
# Sample Configuration File for CSFS #
# #
# #
####################################################################################################
DATA_FILE <data_file> # Paths are relative to the location of the executable
CUTS_FILE # Leave the value blank for this if there is no cut file
# (The file extensions do not matter)
RISK true # Set to true to find risk patterns, false to find protective patterns
NUM_CASES <num_cases> # The number of cases in the dataset
NUM_CTRLS <num_ctrls> # The number of controls in the dataset
NUM_EXPRS <num_exprs> # The number of gene/protein expressions in the dataset
NUM_HEAD_ROWS 1 # The number of header rows in the dataset
NUM_HEAD_COLS 1 # The number of header columns in the dataset
PATTERN_SIZE <ps> # The number of marker states in the genetic pattern(s) to be found
USE_LOWER_CUTOFF false # If true, then the CSSF incumbent solution will be provided to CPLEX.
# Only solutions higher than the incumbent solution will be found.
# If false, then CPLEX will solve the MIP, regardless of the objective value.
# USE_LOWER_CUTOFF and USE_SOLUTION_POOL_THRESHOLD cannot both be true.
USE_SOLUTION_POOL_THRESHOLD true # If true, then all patterns with objective values greater than
# or equal to SOLUTION_POOL_THRESHOLD will be found.
# If false, then only the optimal solution is guaranteed to be
# found.
SOLUTION_POOL_THRESHOLD <threshold> # Does nothing if USE_SOLUTION_POOL_THRESHOLD is false
STARTING_LOWER_BOUND 0 # Starting upper and lower bounds can be provided if they are known ahead
STARTING_UPPER_BOUND 1 # of time. If they are not known, then set STARTING_LOWER_BOUND to 0 and
# STARTING_UPPER_BOUND to 1
QUIET false # Set to true to show only the most important output
VERBOSE false # Set to true to see all output
# QUIET and VERBOSE cannot both be set to true at the same time.
PRINT_CPLEX_OUTPUT false # Set to true to see CPLEX output
TOL 0.000001 # Tolerance value for CPLEX
ID_PREFIX GI
MISSING_SYMBOL NA
CPLEX_SEED 100
USE_SPARSE_CONTRAINTS true # Check for additional contraints to the sparse problem
NUM_BINS 2 # Number of bins, from HIGH, NORM, LOW, NOT_HIGH, and NOT_LOW to be used
USE_HIGH true # Set to true if HIGH variable will be used in pattern
USE_NORM false # Set to true if NORM variable will be used in pattern
USE_LOW true # Set to true if LOW variable will be used in pattern
USE_NOT_HIGH false # Set to true if NOT_HIGH variable will be used in pattern
USE_NOT_LOW false # Set to true if NOT_LOW variable will be used in pattern
HIGH_VALUE 1 # Value of HIGH region in expression data
NORM_VALUE 0 # Value of NORM region in expression data
LOW_VALUE -1 # Value of LOW region in expression data
NOT_LOW_VALUE 0 # Value of NOT_LOW region in expression data
NOT_HIGH_VALUE 0 # Value of NOT_HIGH region in expression data
SET_NA_TRUE true # Set true if NA expression data will result in all bins set to true
# Set false if NA expression data will result in all bins set to false