FilterParam-class: Container for the common criteria used to filtering genomic...

In rscharpf/VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

Description

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.

Usage

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)

Arguments

probability	minumum probability for the call
numberFeatures	minumum number of SNPs/nonpolymorphic features in a region
seqnames	the seqnames (character string or Rle to keep)
state	character: the HMM states to keep
width	the minimum widht of a region
object	a FilterParam object

Slots

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

See Also

cnvFilter cnvSegs hmm2

Examples

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"))

rscharpf/VanillaICE documentation built on May 15, 2019, 5:51 p.m.