chicSignificantInteractions (version 3.7.2+galaxy0)

The interaction data file created by chicViewpoint:

P-value of interaction to be accepted as significant:

List of chromosomes or a BED file containg regions:

Loose p-value:

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

Background model:

The background file computed by chicViewpointBackgroundModel

Minimum interactions:

The minimum number of interactions a detected peaks needs to have to be considered.

Process matrices independently or combine always two (for differential analysis preparation):

Upstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Downstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Clip background distance:

Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.

Truncate zeros by setting them to one.:

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.

Significant interaction detection

Significant interactions are detected by this tool for each viewpoint based on the background model. chicSignificantInteractions outputs for each viewpoint a file containing all recorded significant interactions and a target file. The target file is especially useful in the batch mode context, as it merges for two consecutive listed control and treatment viewpoint 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 based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold --pValue are accepted as a significant interaction.

For more information about HiCExplorer please consider our documentation on readthedocs.io