calculateCnSE {VanillaICE} | R Documentation |
Calculates SNP-specific standard errors for copy number using a reference set.
calculateCnSE(object, referenceSet, epsilon = 0.1)
object |
An object of class SnpCopyNumberSet or
oligoSnpSet . |
referenceSet |
An object of class SnpCopyNumberSet or
oligoSnpSet . If missing, this function uses the samples in
the object to estimate across sample standard deviations |
epsilon |
minimum standard error |
Calculates SNP-specific standard errors from a reference distribution as the product of the within copy number standard deviation of the sample (test set) and the across samples standard deviation from a reference set. The across samples standard deviation is scaled by the median (e.g., across sample sd = across sample sd/ median(across sample sd)).
A matrix of standard errors
R. Scharpf