setGeneric("changeFDR", valueClass = "CpGannotated", function(annot, FDR) {
standardGeneric("changeFDR")
})
setGeneric("cpg.annotate", valueClass = "CpGannotated", function(datatype = c("array", "sequencing"), object,
what = c("Beta", "M"), arraytype = c("EPICv2", "EPICv1", "EPIC",
"450K"), epicv2Repfilter = c("mean", "sensitivity", "precision",
"random"), epicv2Remap = TRUE, analysis.type = c("differential",
"variability", "ANOVA", "diffVar"), design, contrasts = FALSE,
cont.matrix = NULL, fdr = 0.05, coef, varFitcoef = NULL,
topVarcoef = NULL, ...) {
standardGeneric("cpg.annotate")
})
setGeneric("DMR.plot", function(ranges, dmr, CpGs, what = c("Beta", "M"),
arraytype = c("EPICv2", "EPICv1", "450K"), phen.col,
genome = c("hg19", "hg38", "mm10"), labels = names(ranges),
group.means = FALSE, extra.ranges = NULL, extra.title = names(extra.ranges)) {
standardGeneric("DMR.plot")
})
setGeneric("dmrcate", valueClass="DMResults", function(object, lambda = 1000, C = NULL, pcutoff = "fdr",
consec = FALSE, conseclambda = 10, min.cpgs = 2) {
standardGeneric("dmrcate")
})
setGeneric("extractRanges", valueClass="GRanges", function(dmrcoutput, genome=c("hg19", "hg38", "mm10")) {
standardGeneric("extractRanges")
})
setGeneric("rmSNPandCH", function(object, dist = 2, mafcut = 0.05, and = TRUE, rmcrosshyb = TRUE, rmXY = FALSE) {
standardGeneric("rmSNPandCH")
})
setGeneric("rmPosReps", function(object, filter.strategy= c("mean", "sensitivity","precision","random")) {
standardGeneric("rmPosReps")
})
setGeneric("sequencing.annotate", valueClass = "CpGannotated", function(obj, methdesign, all.cov=FALSE, contrasts = FALSE,
cont.matrix = NULL, fdr = 0.05, coef, ...) {
standardGeneric("sequencing.annotate")
})
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