data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")
## Estimate the relative variance ratio factors of cell lines.
# \donttest{
# Perform the MA normalization and construct bioConds to represent cell
# lines.
norm <- normalize(H3K27Ac, 4, 9)
norm <- normalize(norm, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
conds <- list(GM12890 = bioCond(norm[4], norm[9], name = "GM12890"),
GM12891 = bioCond(norm[5:6], norm[10:11], name = "GM12891"),
GM12892 = bioCond(norm[7:8], norm[12:13], name = "GM12892"))
autosome <- !(H3K27Ac$chrom %in% c("chrX", "chrY"))
conds <- normBioCond(conds, common.peak.regions = autosome)
# Automatically select the base bioCond.
estimateVarRatio(conds)
# Explicitly specify the base bioCond.
estimateVarRatio(conds, base.cond = "GM12891")
# }
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