Container for the common criteria used to filtering genomic ranges
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.
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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)
minumum probability for the call
minumum number of SNPs/nonpolymorphic features in a region
the seqnames (character string or
character: the HMM states to keep
the minimum widht of a region
a length-one numeric vector indicating the minimum posterior probability for the called state. Genomic intervals with posterior probabilities below
probabilitywill be filtered.
a positive integer indicating the minimum number of features in a segment
a character vector of
seqnamesto select (i.e., 'chr1' for only those intervals on chromosome 1)
positive integer indicating the minimal width of genomic intervals
character string indicating which hidden Markov model states to select
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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"))
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