chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. For this either Fisher’s test or the chi2 contingency test can be used. The file that is accepted for this test can be created with chicAggregateStatistic. H0 assumes the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected.

usage: chicDifferentialTest --aggregatedFile AGGREGATEDFILE --alpha ALPHA
                            [--outFileName OUTFILENAME]
                            [--statisticTest {fisher,chi2}]
                            [--threads THREADS] [--help] [--version]

Required arguments

--aggregatedFile, -af

path to the aggregated files which should be used for the differential test.

--alpha, -a

define a significance level (alpha) for accepting samples

Optional arguments

--outFileName, -o

Output file for the differential results (Default: “differentialResults.hdf5”).

Default: “differentialResults.hdf5”


Possible choices: fisher, chi2

Type of test used: fisher’s exact test or chi2 contingency (Default: “fisher”).

Default: “fisher”

--threads, -t

Number of threads (uses the python multiprocessing module) (Default: 4).

Default: 4


show program’s version number and exit