Description Usage Arguments Slots See Also Examples

The maximum a posteriori estimate of the trio copy number state for
each genomic range is represented in a
`GRanges`

-derived class. Ultimately, these ranges will
be filtered based on the trio copy number state (e.g., denovo
deletions), size, number of features (SNPs), or chromosome.
`FilterParam`

is a container for the parameters commmonly used
to filter the genomic ranges.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
FilterParam(
probability = 0.99,
numberFeatures = 10,
seqnames = paste0("chr", c(1:22, "X", "Y")),
state = as.character(1:6),
width = 1L
)
## S4 method for signature 'FilterParam'
probability(object)
## S4 method for signature 'FilterParam'
state(object)
## S4 method for signature 'FilterParam'
show(object)
``` |

`probability` |
minumum probability for the call |

`numberFeatures` |
minumum number of SNPs/nonpolymorphic features in a region |

`seqnames` |
the seqnames (character string or |

`state` |
character: the HMM states to keep |

`width` |
the minimum widht of a region |

`object` |
a |

`probability`

a length-one numeric vector indicating the minimum posterior probability for the called state. Genomic intervals with posterior probabilities below

`probability`

will be filtered.`numberFeatures`

a positive integer indicating the minimum number of features in a segment

`seqnames`

a character vector of

`seqnames`

to select (i.e., 'chr1' for only those intervals on chromosome 1)`width`

positive integer indicating the minimal width of genomic intervals

`state`

character string indicating which hidden Markov model states to select

1 2 3 4 5 6 7 8 9 | ```
fp <- FilterParam()
width(fp)
numberFeatures(fp)
seqnames(fp)
## To select CNV segments for which
## - the CNV call has a 'posterior' probability of at least 0.95
## - the number of features is at least 10
## - the HMM states are 1 (homozygous deletion) or 2 (hemizygous deletion)
FilterParam(probability=0.95, numberFeatures=10, state=c("1", "2"))
``` |

VanillaICE documentation built on Nov. 8, 2020, 7:33 p.m.

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