gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
GNU General Public License v3.0
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Intuitive understanding of `txnE` and `txnStrength` #97

Closed ilykos closed 2 years ago

ilykos commented 2 years ago

Is there a formula or ratio of how the txnE and txnStrength parameters should relate to the bin width? Should these always kept at default value or is there a rule of thumb for this parameter?

Quote from snakefile:

# control segmentation - higher (e.g. 0.9999999) leads to higher specificity and fewer segments
# lower (e.g. 0.99) leads to higher sensitivity and more segments
ichorCNA_txnE:  0.9999

# control segmentation - higher (e.g. 10000000) leads to higher specificity and fewer segments
# lower (e.g. 100) leads to higher sensitivity and more segments
ichorCNA_txnStrength:  500