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Matriz Trinucleotide

trinucleotideMatrix

Short description

Builds the 96-trinucleotide context matrix for all single-nucleotide variants (SNVs) in a PyMutation object, enriching the original data with context annotations to enable downstream signature analysis.

Signature

def trinucleotideMatrix(
    self,
    fasta_file: str
) -> Tuple[pd.DataFrame, pd.DataFrame]:

Parameters

Parameter Type Required Description
fasta_file str (path) Yes Path to the reference-genome FASTA file used to look up trinucleotide contexts (must be indexed).

Return value

A tuple (contexts_df, enriched_data):

  • contexts_df – pd.DataFrame of shape 96 × N-samples. Each row corresponds to one of the 96 canonical trinucleotide mutation classes; each column contains the raw counts for a sample.

  • enriched_data – original mutation table with three extra columns:

  • trinuc – the reference trinucleotide (e.g. "ACA").

  • class96 – class label in the form "A[C>T]A".
  • idx96 – integer index (0–95) into the standard context order.

Both DataFrames are never None.

Exceptions

  • ImportError – pyfaidx is missing.
  • ValueError – required columns are absent, no valid SNVs are found, or the FASTA cannot be read.

Minimal usage example

from pymutation import PyMutation           # hypothetical package
mut = PyMutation.from_maf("my_cohort.maf")  # load variants
ctx, enriched = mut.trinucleotideMatrix("GRCh38.fa")
print(ctx.head())