ALLCools.reptile
Contents
ALLCools.reptile¶
Submodules¶
Package Contents¶
- class REPTILE(output_path, train_regions, dmr_regions, train_region_labels, train_sample, bigwig_table, chrom_size_path, window_size=2000, step_size=200, dmr_slop=150, fillna_by_zero=None)[source]¶
- generate_region_ds(self)¶
- property train_region_ds(self)¶
- property train_dmr_ds(self)¶
- property query_region_ds(self)¶
- property query_dmr_ds(self)¶
- property region_model(self)¶
- property dmr_model(self)¶
- _validate_region_name(self, name)¶
- annotate_by_bigwigs(self, name, slop, cpu, redo=False)¶
- _filter_na_train(self, name, sample, max_na_rate=0.5)¶
- prepare_training_input(self, name)¶
- static auto_ml(data, label, output_path, train_size=0.75, random_state=42, cpu=1, tpot_generations=5, tpot_max_time_mins=60, **tpot_kwargs)¶
- _train(self, region_dim, slop, cpu, **kwargs)¶
- train_region_model(self, slop=None, cpu=1, **kwargs)¶
- train_dmr_model(self, slop=None, cpu=1, **kwargs)¶
- fit(self, cpu=10, **kwargs)¶
Convenient function to train everything by default parameters
- _predict(self, region_dim, cpu, mask_cutoff)¶
- predict(self, cpu, mask_cutoff=0.3, bw_bin_size=10, enhancer_cutoff=0.7)¶
- _dump_sample(self, sample, mask_cutoff, bw_bin_size)¶
- dump_bigwigs(self, cpu, mask_cutoff, bw_bin_size)¶
- call_enhancers(self, threshold=0.7, merge_dist=None)¶