cnvFilter {VanillaICE} | R Documentation |
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.
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")) ## S4 method for signature 'HMM' cnvSegs(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6)))) ## S4 method for signature 'HMMList' segs(object) ## S4 method for signature 'HMMList' hemizygous(object) ## S4 method for signature 'HMMList' homozygous(object) ## S4 method for signature 'HMMList' duplication(object) ## S4 method for signature 'HMMList' cnvSegs(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6)))) ## S4 method for signature 'HMMList' cnvFilter(object, filters = FilterParam()) ## S4 method for signature 'HmmGRanges' cnvSegs(object, filters = FilterParam(state = as.character(c(1, 2, 5, 6))))
object |
see |
filters |
a |
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)