ExomeDepth (version 1.1.15)

ExomeDepth-class: Class ExomeDepth

Description

A class to hold the read count data that is used by ExomeDepth to call CNVs.

Objects from the Class

Objects can be created by calls of the form new("ExomeDepth", data = NULL, test, reference, formula = 'cbind(test, reference) ~ 1', subset.for.speed = NULL). data is optional and is only used if the formula argument refers to covariates (in which case these covariates must be included in the data frame). test and reference refer to the read count data for the test and reference samples. Creating a ExomeDepth object will automatically fit the beta-binomial model (using routines from the aod package) and compute the likelihood for the three copy number states (normal, deletion and duplication).

References

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Plagnol et al 2012

See Also

?select.reference.set ?CallCNVs

Examples

# NOT RUN {
showClass("ExomeDepth")
# }