pycallingcards.tools.DE_pvalue#

pycallingcards.tools.DE_pvalue(number1, number2, total1, total2, method='fisher_exact', alternative='greater')[source]#

Compare the peak difference between two groups for specific peak.

Parameters:

  • number1 (int) – The total number of insertions (or the number of cells that contain insertions) in group 1.

  • number2 (int) – The total number of insertions (or the number of cells that contain insertions) in group 2.

  • total1 (int) – The total number of cells in group 1.

  • total2 (int) – The total number of cells in group 2.

  • method (Optional[Literal['binomtest', 'binomtest2', 'fisher_exact']] (default: 'fisher_exact')) – The default method is ‘fisher_exact’, binomtest uses binomial test, binomtest2 uses binomial test but stands on different hypothesis of binomtest, ‘fisher_exact’ uses fisher exact test.

  • alternative (Optional[Literal['two-sided', 'greater']] (default: 'greater')) – If it has two samples/cluster, ‘two-sided’ is recommended. Otherwise, please use ‘greater’.

Returns:

Pvalue for the specific hypothesis.

Example:

>>> import pycallingcards as cc
>>> cc.tl.DE_pvalue(10,456,261,491)