Metagene

Metagene calculation and plotting related methods.

class Metagene

__init__(report_df: DataFrame, **kwargs)

Base class for Bismark data.

Parameters:

• report_df – pl.DataFrame with cytosine methylation status.

• upstream_windows – Number of upstream windows. Required.

• gene_windows – Number of gene windows. Required.

• downstream_windows – Number of downstream windows. Required.

• strand – Strand if filtered.

• context – Methylation context if filtered.

• plot_data – Data for plotting.

Methods

from_bismark	Constructor for Metagene class from Bismark coverage2cytosine report.
from_cgmap	Constructor for Metagene class from BSSeeker2 CGmap file.
from_bedGraph	Constructor for Metagene class from .bedGraph file.
from_coverage	Constructor for Metagene class from .cov file.
from_binom	Constructor for Metagene class from BinomialData.preprocess() .parquet file.
filter	Method for filtering metagene.
resize	Mutate DataFrame to fewer fragments.
trim_flank	Trim Metagene flanking regions.
line_plot	Create LinePlot method.
contexts_line_plot
heat_map	Create HeatMap method.
context_box_plot
cluster	Cluster regions with hierarchical clustering, by their methylation pattern.

class MetageneFiles

Methods

__init__(samples, labels: list[str] | None = None)

from_list	Create istance of MetageneFiles from list of paths.
filter	Metagene.filter() all metagenes.
resize	Metagene.resize() all metagenes.
trim_flank	Metagene.trim_flank() all metagenes.
merge	Merge MetageneFiles into single Metagene
line_plot	Create LinePlotFiles method.
heat_map	Create HeatMapNew method.
box_plot
cluster	Cluster samples regions by methylation pattern.
dendrogram	Cluster samples by total methylation level of regions and draw dendrogram.