VanillaICE (version 1.34.0)

cnvFilter: Filter the HMM-derived genomic ranges for copy number variants

Description

The HMM-derived genomic ranges are represented as a GRanges-derived object. cnvFilter returns a GRanges object using the filters stipulated in the filters argument.

Usage

cnvFilter(object, filters = FilterParam())
cnvSegs(object, filters = FilterParam(state = c("1", "2", "5", "6")))
duplication(object, filters = FilterParam(state = c("5", "6")))
deletion(object, filters = FilterParam(state = c("1", "2")))
hemizygous(object, filters = FilterParam(state = "2"))
homozygous(object, filters = FilterParam(state = "1"))
"cnvSegs"(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6))))
"segs"(object)
"hemizygous"(object)
"homozygous"(object)
"duplication"(object)
"cnvSegs"(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6))))
"cnvFilter"(object, filters = FilterParam())
"cnvSegs"(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6))))

Arguments

object

see showMethods(cnvFilter)

filters

a FilterParam object

See Also

FilterParam

Examples

data(snp_exp)
fit <- hmm2(snp_exp)
segs(fit) ## all intervals
cnvSegs(fit)
filter_param <- FilterParam(probability=0.95, numberFeatures=10, state=c("1", "2"))
cnvSegs(fit, filter_param)
filter_param <- FilterParam(probability=0.5, numberFeatures=2, state=c("1", "2"))
cnvSegs(fit, filter_param)
hemizygous(fit)
homozygous(fit)
duplication(fit)