Description Usage Arguments Author(s)
For each parental read counts you have, add this to
{obj_offspring}
to get the objective function.
1 2 3 | obj_parent(pcounts, psize, ploidy, pgeno, bias_val = 1, seq_error = 0,
od_param = 0, outlier = FALSE, out_prop = 0.01, out_mean = 0.5,
out_disp = 1/3, weight = 1)
|
pcounts |
The number of counts of the reference allele we observe in a parent. |
psize |
The total number of reads we observe in a parent. |
ploidy |
An integer. The ploidy of the species. This is assumed to be the same for each individual. |
pgeno |
The genotype of the parent. |
bias_val |
The bias parameter. A value of 1 means there is no bias toward one allele or the other. A value less than one indicates a bias toward the reference allele. A value greater than one indicates a bias toward the non-reference allele. |
seq_error |
The sequencing error rate. |
od_param |
The overdispersion parameter in the beta-binomial model for the OK counts. When this is zero, this resorts to the binomial model for counts. |
outlier |
A logical. Should we include an outlier model ( |
out_prop |
The proportion of points that are outliers. Defaults
(quite arbitrarily) to |
out_mean |
The mean of beta-binomial for the outlier distribution.
Defaults to |
out_disp |
The overdispersion parameter of the outlier distribution.
Defaults to |
weight |
A double that multiplies to the log-likelihood (objective).
Should only be used when |
David Gerard
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