LL: Likelihood of cfDNA read being tumor or nomal derived
In ndbrown6/EMseq: Enzymatic Methylation sequencing

Description Usage Arguments Value Note Author(s) See Also

Returns the likelihood of a cfDNA read being tumor or normal derived

1	LL(p, n, a_hat, b_hat)

`p`	scalar between 0 and 1 describing the observed proportion of methylated CpG sites in the cfDNA read
`n`	integer greater than 1 indicating the number of CpG sites being considered
`a_hat`	scalar greater than 0 indicating the shape parameter of beta distribution
`b_hat`	scalar greater than 0 indicating the shape parameter of beta distribution

Invisibly the value of the likelihood

a_hat and b_hat describe the shape parameters of a Beta(a, b) distribution for a set n CpG sites. The choice of values for a_hat and b_hat should be informed by the proprotion of methylated CpG sites in a training set of tumor and normal derived gDNA. Please refer to Figure 3 in Li et al. (2018) https://doi.org/10.1093/nar/gky423. Reasonable estimates can be obtained using the utility functions in this package.

David Brown
brownd7@mskcc.org

betaABfromMeanKappa betaABfromMeanSD betaABfromModeKappa

ndbrown6/EMseq documentation built on Jan. 20, 2021, 2:36 a.m.