Description Usage Arguments See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | 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 |
1 2 3 4 5 6 7 8 9 10 11 | 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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