MethylSeg Components Example

Use the assigner, analyzer, and segmentor directly after loading a saved pathway.

This example loads a packaged saved model so that the focus stays on the demonstrated operation.

[1]:

from pathlib import Path

from methylseg import MethylSegPathway, MethylStateAssignmentMethod, MethylationStates
from methylseg.helper_classes import DATA_DIR

[2]:

REFERENCE_DIR = DATA_DIR / "reference_files"
OUTPUT_ROOT = Path("out")
CHROM = "chr1"

RESOLUTION = "450k"
SAMPLE_NAME = "TCGA-BD-A3EP-01A"
SAMPLE_FILE = REFERENCE_DIR / "TCGA-BD-A3EP-01A_450k.tsv.gz"
OUT_DIR = OUTPUT_ROOT / "methylseg_components_example"

Load a saved model and prepare the sample

[3]:

model = MethylSegPathway.get_pretrained_model(
    out_dir=OUT_DIR,
    resolution=RESOLUTION,
)
sample_info, removed_df = MethylSegPathway.prepare_sample_info(
    sample_name=SAMPLE_NAME,
    sample_file=SAMPLE_FILE,
    resolution=RESOLUTION,
    min_coverage=10,
)
sample_info.sample_id

[3]:

'TCGA-BD-A3EP-01A'

Assigner

[4]:

assigner = model.assigner
meth_data, emissions, pca_scores, _, _, labels = assigner.apply_kmeans_to_sample(
    sample_info=sample_info, chrom=CHROM
)
assigner.plot_embedding(
    emission_df=emissions, labels=labels, meth_data=meth_data, sample_info=sample_info,
    chrom=CHROM, method="pca", hexbin=True, hexbin_mincnt=1,
)

../../_images/tutorials_generated_05_methylseg_components_example_6_0.png

[4]:

../../_images/tutorials_generated_05_methylseg_components_example_6_1.png

Analyzer

[5]:

rule_labels = model.analyzer.define_states_by_rules(
    sample_info=sample_info, chrom=CHROM, sample_emissions=emissions
)

Segmentor

[6]:

segmented_meth, _ = model.segmentor.segment_sample(sample_info=sample_info, chrom=CHROM)
regions_chr1 = model.segmentor.create_regions()
regions_chr1.head()

[6]:

	CpG_chrm	start	end	avg_beta	probe_count	state
0	chr1	69590	859174	0.432264	53	PMD
1	chr1	859718	899435	0.504805	77	INTERMEDIATE
2	chr1	900423	931328	0.406957	46	PMD
3	chr1	933305	956300	0.463662	71	INTERMEDIATE
4	chr1	956798	990294	0.819857	70	HIGH