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

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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))))

Arguments

object

see showMethods(cnvFilter)

filters

a FilterParam object

See Also

FilterParam

Examples

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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)

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