chicSignificantInteractions

Per viewpoint the significant interactions are detected based on the background model. For each viewpoint file, an output file is created with all recorded significant interactions and a target file. The target file is especially useful in the batch mode context; for two consecutive listed control and treatment viewpoints it merges the significant interactions which can then be used to test for a differential interaction scheme.

chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional p-value is computed based on the sum of interactions for this neighborhood. Only interactions with a higher p-value (as specified by the threshold –pValue) are accepted as a significant interaction.

usage: chicSignificantInteractions --interactionFile INTERACTIONFILE --pValue
                                   PVALUE
                                   [--xFoldBackground XFOLDBACKGROUND | --loosePValue LOOSEPVALUE]
                                   --backgroundModelFile BACKGROUNDMODELFILE
                                   --range RANGE RANGE
                                   [--outFileNameSignificant OUTFILENAMESIGNIFICANT]
                                   [--outFileNameTarget OUTFILENAMETARGET]
                                   [--combinationMode {dual,single}]
                                   [--threads THREADS] [--truncateZeroPvalues]
                                   [--fixateRange FIXATERANGE]
                                   [--peakInteractionsThreshold PEAKINTERACTIONSTHRESHOLD]
                                   [--help] [--version]

Named Arguments

--xFoldBackground, -xf

Filter x-fold over background. Used to merge neighboring bins with a broader peak but less significant interactions to a single peak with high significance. Used only for pValue option.

--loosePValue, -lp

loose p-value threshold to filter target regions in a first round. Used to merge neighboring bins with a broader peak but less significant interactions to a single peak with high significance. Used only for pValue option.

Required arguments

--interactionFile, -if

path to the interaction file (HDF5) which should be used for aggregation of the statistics.

--pValue, -p

p-value threshold to filter target regions for inclusion in differential analysis.

--backgroundModelFile, -bmf

path to the background file.

--range

Defines the region upstream and downstream of a reference point which should be included. Format is –region upstream downstream, e.g. –region 500000 500000 plots 500kb up- and 500kb downstream. This value should not exceed the range used in the other chic-tools.

Optional arguments

--outFileNameSignificant, -os

File name suffix to save the results; prefix is the input file name (Default: “significantInteractions.hdf5”).

Default: “significantInteractions.hdf5”

--outFileNameTarget, -ot

The file to store the target data (Default: “targetFile.hdf5”).

Default: “targetFile.hdf5”

--combinationMode, -cm

Possible choices: dual, single

This option defines how the interaction data should be computed and combined: dual: Combines as follows: [[matrix1_gene1, matrix2_gene1], [matrix2_gene1, matrix3_gene1],[matrix1_gene2, matrix2_gene2], …]single: Combines as follows: [matrix1_gene1, matrix1_gene2, matrix2_gene1, …], (Default: “dual”).

Default: “dual”

--threads, -t

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

Default: 4

--truncateZeroPvalues, -tzpv

Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision.

Default: False

--fixateRange, -fs

Fixate range of backgroundmodel starting at distance x. E.g. all values greater than 500kb are set to the value of the 500kb bin (Default: 500000).

Default: 500000

--peakInteractionsThreshold, -pit

The minimum number of interactions a detected peak needs to have to be considered (Default: 5).

Default: 5

--version

show program’s version number and exit