scphylo.tl.sphyr#

scphylo.tl.sphyr(df_input, alpha, beta, n_restarts=10, n_threads=1, time_limit=None, n_cell_clusters=10, n_mut_clusters=15)[source]#

Solving using SPhyR.

Tumor phylogeny estimation from single-cell sequencing data under loss and error [SPhyR].

Parameters

  • df_input (pandas.DataFrame) – Input genotype matrix in which rows are cells and columns are mutations. Values inside this matrix show the presence (1), absence (0) and missing entires (3).

  • alpha (float) – False positive error rate.

  • beta (float) – False negative error rate.

  • n_restarts (int, optional) – Number of threads, by default 10

  • n_threads (int, optional) – Number of threads, by default 1

  • time_limit (int, optional) – Time limit (in seconds), by default None

  • n_cell_clusters (int, optional) – Number of cell clusters, by default 10

  • n_mut_clusters (int, optional) – Number of mutation clusters, by default 15

Returns

A conflict-free matrix in which rows are cells and columns are mutations. Values inside this matrix show the presence (1) and absence (0).

Return type

pandas.DataFrame

Examples#

Reconstruct tree by SPhyR

Reconstruct tree by SPhyR