Accessors for batch-specific summary statistics.
The summary statistics stored here are used by the tools for copy number estimation.
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An object of class
An array with dimension R x A x G x C, or R x G x C.
R: number of markers A: number of alleles (2) G: number of biallelic genotypes (3) C: number of batches
Ns returns an array of genotype frequencies stratified by
batch. Dimension R x G x C.
corr returns an array of within-genotype correlations
(log2-scale) stratified by batch. Dimension R x G x C.
medians returns an array of the within-genotype medians
(intensity-scale) stratified by batch and allele. Dimension R x A x G
mads returns an array of the within-genotype median absolute
deviations (intensity-scale) stratified by batch and allele. Dimension
is the same as for
tau2 returns an array of the squared within-genotype median
absolute deviation on the log-scale. Only the mads for AA and BB
genotypes are stored. Dimension is R x A x G x C, where G is AA or
BB. Note that the mad for allele A/B for subjects with genotype BB/AA
is a robust estimate of the background variance, whereas the the mad
for allele A/B for subjects with genotype AA/BB is a robust estimate
of the variance for copy number greater than 0 (we assume that on the
log-scale the variance is rougly constant for CA, CB > 0).
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data(cnSetExample) Ns(cnSetExample)[1:5, , ] corr(cnSetExample)[1:5, , ] meds <- medians(cnSetExample) mads(cnSetExample)[1:5, , ,] tau2(cnSetExample)[1:5, , ,]