Description Usage Arguments Value Author(s) Examples
Computes a (normalized) likelihood for each of the three possible genotypes (i.e. AA, AB, and BB) of a diploid individual at a given biallelic site.
1 | normGL(x, error, callthreshold, coding)
|
x |
(character vector) specifies the observed counts of the reference allele (allele A) and alternative allele (allele B) at a site for a diploid individual |
error |
(numeric float) specifies a fix sequencing error rate (errors that may have been introduced in base calling, alignment and assembly. This value may range from 0 to 1. For an error rate of 1 percent, enter 0.01. |
callthreshold |
(numeric float; optional) only call genotypes with a posterior probability (calculated assuming a uniform prior) of >callthreshold. If no posterior probability is greater than the callthreshold, the function returns NA. If no argument is specified, the function returns the normalized likelihoods (or equivalently, the posterior probabilities calculated assuming a uniform prior on the three genotypes) for all three genotypes. |
coding |
(character) specifies the format of the function output. The user may select either 'character' or 'numeric'. |
Refer to paramemter callthreshold and coding.
Ariel W Chan, ac2278@cornell.edu
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