scphylo.pp.bifiltering

scphylo.pp.bifiltering(df, cellr, mutr, time_limit=3600)

Bi-filtering to find maximally inforemed submatrix.

This function runs an ILP to find maximally inforemed submatrix where the number of mutant genotypes is maximized.

Parameters:

• df (pandas.DataFrame) – The input noisy genotype matrix where entries are 0,1 and 3.

• cellr (float) – ratio for picking how many cells.

• mutr (float) – ratio for picking how many mutations.

• time_limit (int, optional) – Time limit for the ILP solver, by default 3600.

Returns:

The output gentoype submatrix.

Return type:

pandas.DataFrame