epiout.annotate
Module Contents
Classes
Annotate peaks with epigenetic data. |
|
- class epiout.annotate.EpiAnnot(config: str, gtf: str = None, chrom_sizes: str = None, counts: str = None, gene_types: set = ('protein_coding',), hic_bin_vicinity=200, hic_normalization='NONE', hic_binsize=5000, hic_min_read=10)
Annotate peaks with epigenetic data.
- Parameters
config – Path to annotation config file.
gtf – Path to GTF file.
counts – Path to counts table.
gene_types – Genes to use in the annotation.
hic_bin_vicinity – Distance to search for HIC bins.
hic_normalization – HIC normalization method.
hic_binsize – HIC binsize.
hic_min_read –
- _read(self)
- _read_bed(self, files)
- _read_counts(self, counts)
- _co_outliers(self, outliers)
- annotate(self, gr)
Annotate peaks for chromatin features.
- Parameters
gr – genomic intervals as pyranges
- _annotate_feature(self, df, df_gtf)
- _tss_proximal(self, df_gtf)
- _has_chipseq(self, df, mark)
- _chipseq_marks(self, df, mark)
- _annotate_grs(self, gr)
- annotate_hic(self, gr)
Annotation of HIC contacts.
- Parameters
gr – genomic intervals as pyranges
- _neighbors(self, gr)
- _abc_score(self, df)
- save_annotate(self, gr, output_prefix)
Annotate peaks and save results.
- class epiout.annotate.GTFAnnot(gtf_file: str, gene_types: set = ('protein_coding',), tss_upstream=1000, upsteam=10000, downstream=1000)
- read_features(self, gtf_file, gene_types)
Read features from gtf file
- Parameters
gtf_file – Path to gtf file.
gene_type – Gene types to consider protein_coding.
- annotate(self, gr: Union[str, pyranges.PyRanges])
Annotate peaks for gtf features.