aspu implemented in julia
Adaptive Sum of Powered Scores (aSPU)
Reference: doi:10.1002/gepi.21931
Contact: Antoine Baldassari baldassa@email.unc.edu
Requires Julia 1.0+
Will install Julia packages: ClusterManagers, CSV, Distributions
Computes aggregate p-values from multiple traits, using GWAS results.
Input is a comma-separated file with a header, with SNP names in the
first column, and each subsequent column containing summary z-scores.
Output is comma-separated, with columns for SNP name, aspu p-value,
and best-powered gamma value
The log file will be named aspu_julia_<timestamp>.out
USAGE
bash aspu_slurm.sh --ncpu int --filein filename --logB int ...
Example: bash aspu_slurm.sh --ncpu 10 --filein myfile.csv --logB 6
--fileout yaymath.txt --slurm "--begin=now+1hour"
--name myaspuresults
ARGUMENTS
--name dirname [default: aspu_run_date_time]
Name of directory where results will be stored.
--filein filename (REQUIRED)
path to input file
--logB integer between 1 and 9 (REQUIRED)
log10 of the number of Monte-Carlo simulations
For example, --logB 8 will allow the algorithm to run up to 10^8
simulations, allowing p-values as small as 10^-8
--ncpu integer (REQUIRED)
The number of CPUs to request from the cluster
(more than 20 is likely overkill)
--fileout filename
Name of output file.
The default is aspu_results_<timestamp>_1E<logB>.csv
--incov filename
Specify own (comma-separated) file containing covariance matrix
of z-scores. The default is to calculate if from input results
--outcov filename
Specify name of output z-scores covariance matrix
--norun
Stop program after setup phase. Used to check for mistakes and
verify arguments before commiting to full run (check log).
--slurm string
SLURM options to pass to sbatch. Must be enclosed in " or ' quotes
and cannot conflict with options -n, --mem-per-cpu, --cpus-per-task,
and -o
--pows
Specify powers to be used. Integer powers must be ranges, or
comma-separated integers.
The integer 9 is a special value reserved for gamma=infty (MinP)
Example: 1:5,9
Default is 1:9
--testnow
Run aspu in the local session instead of submitting using SLURM
For testing.