NAMESPACE

useDynLib(COHCAP)

import(WriteXLS, COHCAPanno, RColorBrewer, gplots, Rcpp, BH, RcppArmadillo)

importFrom("grDevices", "colorRampPalette", "colors", "dev.off", "pdf")
importFrom("graphics", "abline", "legend", "lines", "par", "plot")
importFrom("stats", "aov", "as.dendrogram", "cor", "cor.test",
           "dendrapply", "density", "dist", "fisher.test", "hclust",
           "is.leaf", "lm", "na.omit", "p.adjust", "prcomp",
           "quantile", "t.test","pt")
importFrom("utils", "data", "head", "read.table", "write.table")
importFrom("stats", "as.dist")

export(COHCAP.annotate,
		COHCAP.qc,
		COHCAP.site,
		COHCAP.avg.by.site,
		COHCAP.avg.by.island,
		COHCAP.integrate.avg.by.site,
		COHCAP.integrate.avg.by.island,
		COHCAP.denovo,
		COHCAP.reformatFinalReport,
		COHCAP.BSSeq.preprocess,
		COHCAP.BSSeq_V2.methyl.table)