FilterParamMD {MinimumDistance} | R Documentation |
A container for criteria used to filter the segmentation results post-hoc. Options including filtering on the posterior call, the posterior probability of the posterior call, the minimum number of markers spanned by the segment, the minimum width of the segment, and chromosome. Convenience functions are available for commonly used filters.
FilterParamMD(state = trioStateNames(), seqnames = paste0("chr", 1:22), ...)
state |
trio copy number states to select |
seqnames |
chromosome names to select |
... |
additional arguments passed to |
library(VanillaICE) data(md_gr) data(md_exp) mdparam <- MinDistParam() fit <- MAP2(md_exp, md_gr, mdparam) ## return all segments segs(fit) ## Default filters param <- FilterParamMD() param cnvFilter(fit, param) param2 <- FilterParamMD(seqnames="chr22", probability=0.9, numberFeatures=10) cnvFilter(fit, param2) denovoHemizygous(fit)