climerlab/sync-greedy

A greedy algorithm to find the combination of features that maximized the Younden J statistic.

sync-greedy

Greedy implementation of the Sync feature selection algorithm.

To Use

Configure the Makefile with the locaion of open mpi libraries and binary

Compile with the Makefile by navigating to the root directory and entering: make

Update configuration file

Run the program. For an example enter: mpirun -np 4 ./sync <cfg_file>

Configuration File

DATA_FILE - Tab seperated file where the first NUM_CASES columns are cases and the next NUM_CTRLS columns are controls. The row indicate features.

SCRATCH_DIR - Directory where ouputs are recorded.

NUM_CASES - Number of cases in DATA_FILE.

NUM_CTRLS - Numbr of controls in DATA_FILE.

NUM_EXPRS - Number of features in DATA_FILE.

NUM_HEAD_ROWS - Number of header rows in DATA_FILE.

NUM_HEAD_COLS - Number of header columns in DATA_FILE.

RISK - Boolean that indicates if risk patterns (true) or protective patterns should be found.

MAX_PS - Maximum pattern size to search.

MIN_OBJ - Minimum Younden J value that will be kept for PS=1 patterns.

USE_SOL_POOL - Boolean that indicates if a solution pool will be kept.

SOL_POOL_SIZE - Size of solution pool to keep.

MISSING_SYMBOL - String used to indicate missing data in DATA_FILE.

SET_NA_TRUE - Boolean used to indicate if missing data is treated as both high and low.

HIGH_VALUE - Value in DATA_FILE that indicates high expression.

NORM_VALUE - Value in DATA_FILE that indicates normal expression.

LOW_VALUE - Value in DATA_FILE that indicates low expression.

Outputs

PS#.solPool - Files containing a collection of patterns of size #

markerPairs.csv - Contains a count of individuals from G_1 that contain each pair of markers

Notes

Requires Open MPI

DATA_FILE should be tab seperate, the columns represent individuals and the rows represent features