iscc.data.bulkDNA ¶

bulkDNA(breadth='wgs', target_genes='all', data_mode='counts', depth_model='dm', n_reads=None, seed=42, batch_label=None, fpr=None, fnr=None, **hyper_overrides)

Bases: DNA

Bulk DNA-seq: pool the sampled cells, high read budget, large-kappa compositional depth, Binomial allele layer.

Coverage at a locus ∝ the POOLED total copy number (Σ_c CN_cl) × per-locus efficiency, so amplified segments draw proportionally more reads, and at a fixed budget compositionally reduce the coverage of others (the DM coupling). The pooled true alt fraction is the copy-number-weighted mean of the per-cell VAFs.

Takes no constructor parameters of its own: it pools every sampled cell (there is no n_cells). The bulk mode_defaults set a large-kappa amplification regime (kappa=2000 ≈ un-amplified multinomial/Poisson) and leave the single-cell allele knobs inert (ado_rate=0, doublet_rate=0).

See DNA for the constructor parameters.

Methods:

Name	Description
`run`	Assay a pooled bulk-DNA sample from the sampled cells.
`to_anndata`	One 'pseudobulk sample' observation × loci (var) AnnData (X = coverage).

run ¶

run(cell_data, cell_subset=None, **kwargs)

Assay a pooled bulk-DNA sample from the sampled cells.

Pools the selected cells into a single bulk library and emits, per locus, the read depth, alternate-allele counts, VAF, and a GC/mappability-corrected copy-number log2 ratio.

Parameters:

Name	Type	Description	Default
`cell_data`	`dict`	Per-cell ground-truth tables from the sampling stage; uses the SNV table `cell_snv` and the copy-number ground truth.	required
`cell_subset`	`array-like of cell IDs`	Restrict the pool to these cells. By default every sampled cell is pooled.	`None`

Returns:

Type	Description
`bulkDNA`	`self`, with the per-locus results in `observed_data`. Call `to_anndata` or `write` to export.

to_anndata ¶

to_anndata()

One 'pseudobulk sample' observation × loci (var) AnnData (X = coverage).

Technology presets¶

Bulk DNA sequencing differs by capture breadth — set breadth:

Assay	`breadth`	Depth (`mu_depth`)	Loci	Dominant capture bias
Whole-genome (WGS)	`"wgs"`	~30×	all	GC curve
Whole-exome (WES)	`"wes"`	~120×	exome (~30% of loci)	per-target
Targeted panel	`"panel"`	~1500×	a small gene panel	per-amplicon