Description Usage Arguments Examples
Assess whether genotype is heterozygous based on BAFs
1 2 3 4 5 6 7 8 9 10 11 12 13 | isHeterozygous(object, cutoff)
## S4 method for signature 'ArrayViews'
isHeterozygous(object, cutoff)
## S4 method for signature 'SnpArrayExperiment'
isHeterozygous(object, cutoff)
## S4 method for signature 'numeric'
isHeterozygous(object, cutoff)
## S4 method for signature 'matrix'
isHeterozygous(object, cutoff)
|
object |
a SnpArrayExperiment or ArrayViews object containing BAFs, a matrix of BAFs, or a numeric vector of BAFs. vector of BAFs |
cutoff |
a length-two numeric vector providing the range of BAFs consistent with allelic heterozygosity |
1 2 3 4 5 6 | if(require("BSgenome.Hsapiens.UCSC.hg18")){
bsgenome <- BSgenome.Hsapiens.UCSC.hg18
snp_exp <- getExampleSnpExperiment(bsgenome)
is_het <- isHeterozygous(snp_exp[, 1], c(0.4, 0.6))
table(is_het)
}
|
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