isHeterozygous {VanillaICE} | R Documentation |
Assess whether genotype is heterozygous based on BAFs
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 |
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) }