pycallingcards.tools.GWAS_adata_bulk#

pycallingcards.tools.GWAS_adata_bulk(adata, number=100, bindings=['Chr', 'Start', 'End'])[source]#

Plot GWAS results for different cell types for bulk calling cards data. It considers the relative number of insertions in each group. GWAS data is downloaded from GWAS Catalog.

Parameters:

  • adata (AnnData) – The anndata object of bulk CC data.

  • number (int (default: 100)) – Default is 100. The minimun total number for each SNP.

  • bindings (list (default: ['Chr', 'Start', 'End'])) – Default is [‘Chr’, ‘Start’, ‘End’]. The name for binding information.

Return type:

DataFrame

Example:

>>> import pycallingcards as cc
>>> adata_cc = cc.datasets.mouse_brd4_data(data="CC")
>>> adata_cc = cc.tl.liftover(adata_cc)
>>> cc.tl.GWAS_adata_bulk(adata_cc, bindings = ['Chr_liftover', 'Start_liftover', 'End_liftover'])