man/batchStatisticAccessors.Rd
 46b837ea  \name{batchStatisticAccessors} \alias{Ns} \alias{corr} \alias{tau2} \alias{mads} \alias{medians} \title{ Accessors for batch-specific summary statistics. } \description{ The summary statistics stored here are used by the tools for copy number estimation. } \usage{ corr(object, ...) tau2(object, ...) mads(object,...) medians(object,...) Ns(object,...) } \arguments{ \item{object}{ An object of class \code{CNSet}.}  1f86c51a  \item{\dots}{Ignored}  46b837ea  } \value{  1f86c51a  An array with dimension R x A x G x C, or R x G x C.  46b837ea  R: number of markers A: number of alleles (2) G: number of biallelic genotypes (3) C: number of batches \code{Ns} returns an array of genotype frequencies stratified by batch. Dimension R x G x C. \code{corr} returns an array of within-genotype correlations (log2-scale) stratified by batch. Dimension R x G x C. \code{medians} returns an array of the within-genotype medians (intensity-scale) stratified by batch and allele. Dimension R x A x G x C. \code{mads} returns an array of the within-genotype median absolute deviations (intensity-scale) stratified by batch and allele. Dimension is the same as for \code{medians}. \code{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). } \seealso{ \code{\link{batchStatistics}} } \examples{  cceffc9c  data(cnSetExample) Ns(cnSetExample)[1:5, , ] corr(cnSetExample)[1:5, , ] meds <- medians(cnSetExample) mads(cnSetExample)[1:5, , ,] tau2(cnSetExample)[1:5, , ,]  46b837ea  } \keyword{manip}