pychromvar.match_motif

pychromvar.match_motif(data: AnnData | MuData, motifs, pseudocounts=0.0001, p_value=5e-05, background: Literal['subject', 'genome', 'even'] = 'even', genome_file: str | None = None)

Perform motif matching to predict binding sites using MOODS.

Parameters:

dataUnion[AnnData, MuData]

AnnData object with peak counts or MuData object with ‘atac’ modality.

motifs_type_

List of motifs

pseudocountsfloat, optional

Pseudocounts for each nucleotide, by default 0.0001

p_value_type_, optional

_description_, by default 5e-05

background_BACKGROUND, optional

Background distribution of nucleotides for computing thresholds from p-value. Three options are available: “subject” to use the subject sequences, “genome” to use the whole genome (need to provide a genome file), or even using 0.25 for each base, by default “even”

genome_filestr, optional

If background is set to genome, a genome file must be provided, by default None

Returns:

Update data.