single-cell-genetics / XClone

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

https://xclone-cnv.readthedocs.io/en/latest/

Apache License 2.0

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ref BAF strategy explore #8

Closed Rongtingting closed 1 month ago

Rongtingting commented 1 year ago

use variance to help keep ref BAF or not
may help to denoise some chrs

Rongtingting commented 1 year ago

can be updated after ref-free version

Rongtingting commented 1 month ago

BAF module without specifying reference cells

update_info_from_rdr: can be set as False to make BAF totally independent.

xconfig = xclone.XCloneConfig(dataset_name = dataset_name, module = "BAF")

xconfig.ref_celltype = None
xconfig.update_info_from_rdr = False
xconfig.theo_neutral_BAF = 0.5