cnvFilter {VanillaICE} | R Documentation

## 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"))

    ## 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

    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)

[Package VanillaICE version 1.46.0 Index]