scphylo.tl.scistree#

scphylo.tl.scistree(df_input, alpha, beta, n_threads=1, experiment=False)[source]#

Solving using ScisTree.

Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach [ScisTree].

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_threads¶ (int) – Number of threads.
experiment¶ (bool, optional) – Is in the experiment mode (the log won’t be shown), by default False

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#