MUTPARAMS.sh~

# Centralized parameter file

# ************************************************************************************
# INPUT OUTPUT
# ************************************************************************************

export MUTATIONMATRIXPATH=/Users/jlu96/conte/jlu/mutex/data/ACC_broad-som.m2

# This will be prefix all of the output files.
export OUTPUTPREFIX=/Users/jlu96/conte/jlu/mutex/output/ACC_broad-som


# ************************************************************************************
# LOADING PARAMETERS
# ************************************************************************************

# Limit to genes mutated in at least this # of patients
export MINFREQ=

# Limit to genes mutated in at least this % of patients
export MINPERCENTILE=2

# Limit to this # of top most frequently mutated genes
export TOP_NUMBER=

# List of patients to limit loading to
export PATIENTFILE=$FOLDER/shared_patients.plst

# List of Genes to limit loading to
export GENEFILE=COSMICGenes_OnlyLoss.txt

# Blacklists
export PATIENTBLACKLIST=
export GENEBLACKLIST=



# ************************************************************************************
# LIMIT WHICH PAIRS TO TEST
# ************************************************************************************

# If GENELIST1 and GENELIST2 are both set, only pairs containing one gene in GENELIST1 and one in
# GENELIST2 will be tested. If only GENELIST1 is set, only pairs containing two genes in GENELIST1
# Will be tested.
export GENELIST1=
export GENELIST2=

# If set, only test pairs from PAIRLIST. The column header must be "Gene0   Gene1"
export PAIRLIST=

# If set, only test genes that are at least this distance away.
# This will only apply to genes ending in "gain" or "loss".
# E.G. Say TP53 and MYC are 30 bp away. If the threshold is set to 1000000, the pair (TP53gain, MYCloss) will not
# be tested. But the pair (TP53, MYCloss) would be tested. This allows only Copy Number pairs to be
# filtered out
export MINDISTANCETHRESHOLD=100000000



# ************************************************************************************
# CALCULATION PARAMETERS
# ************************************************************************************

# Mutex Pair PValue Threshold. Default is 0.05
export MPROB=
# Maximum Overlap between mutually exclusive pairs.
export MAXOVERLAP=


# Cooccur Pair PValue Threshold. Default is 0.05
export CPROB=
# Minimum overlap between cooccurring pairs
export MINCOOCCUR=
# minimum co-occurrence ratio for cooccuring pairs. This is the overlap/
export MINRATIO=


# If "Triplet", search for triplets among pairs. If "Network", calculate Network attributes
export GROUPTYPE=Triplet


# Number of processes to start and divide parameter testing across.
export NUMPROCESSES=3