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