pycallingcards.tools.liftover#

pycallingcards.tools.liftover(data, torlerance=10, original_genome='mm10', new_genome='hg38')[source]#

Use liftover to transform from one genome to another [Hinrichs et al., 2006].

Parameters:

  • data (Union[AnnData, DataFrame]) – pd.DataFrame with the first three columns as chromosome, start and end. Anndata with peak adata.var contains the first three columns as chromosome, start and end.

  • torlerance (int (default: 10)) – The max multiples allowsfor the length of new_genome to compare with the original one.

  • original_genome (str (default: 'mm10')) – The original genome.

  • new_genome (str (default: 'hg38')) – The new genome.

Return type:

Union[AnnData, DataFrame]

Example:

>>> import pycallingcards as cc
>>> adata_cc = cc.datasets.mousecortex_data(data="CC")
>>> adata_cc = cc.tl.liftover(adata_cc)