hicTADClassifier¶
Description¶
Uses Supervised Learning to call TAD boundaries. One or multiple HiC-Matrices can be passed, from which a BED file will be produced containing the predicted boundary positions. By default, a EasyEnsembleClassifier as described in Liu et al.: “Exploratory Undersampling for Class-Imbalance Learning” will be used to call TADs. Internally this classifier relies on Resampling, Boosting and Bagging. Passed matrices will be range normalized by default. Alternatively, obs/exp normalization can be used. Currently, only classifiers for 10kb resolution are implemented. For building own classifiers or tune existing ones, hicTrainClassifier can be used and passed with the saved_classifer argument. A simple usage example can be seen here:
$ hicTADClassifier -m my_matrix.cool -o predictions -n range
usage: hicTADClassifier --matrices MATRICES [MATRICES ...] --out_file OUT_FILE
[OUT_FILE ...]
[--normalization_method {obs_exp,range}]
[--saved_classifier SAVED_CLASSIFIER]
[--unselect_border_cases] [--threads THREADS]
[--chromosomes CHROMOSOMES [CHROMOSOMES ...]] [--help]
[--version]
Required arguments¶
- --matrices, -m
HiC-Matrix file or list of files for input. Only COOLER files are supported!
- --out_file, -o
output file path for predictions
Optional arguments¶
- --normalization_method, -n
Possible choices: obs_exp, range
set the normalization mode, with which the passed matrices will be normalized. If not set, matrices will be range normalized
Default: “range”
- --saved_classifier
Default classifier are available for 10kb, 25kb, 50kb and 100kb resolution. Do not set this parameter to use the default models. Pass a self-trained classifier (from hicTrainTADClassifier) to load a non-default model.
- --unselect_border_cases
set whether genes at the border of the matrices will not be predicted
Default: False
- --threads, -t
number of threads used
Default: 4
- --chromosomes
Chromosomes to include in the analysis. If not set, all chromosomes are included.
- --version
show program’s version number and exit