getDenom-method: getDenom
In ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account

Description Usage Arguments Details Value See Also Examples

Returns the denominator used as the basis for the log-ratio, for an aldex.clr object.

1	getDenom(.object)

.object

A aldex.clr object containing the Monte Carlo Dirochlet instances derived from estimating the technical variance of the raw read count data, along with sample and feature information.

Returns the denominator used to calculate the log-ratios. "all" is the centred log-ratio. "iqlr" is the interquartile log-ratio. A vector of numbers is the offset of the variables used in the denominator

A vector of values.

aldex.clr

data(selex)
    #subset for efficiency
    selex <- selex[1201:1600,]
conds <- c(rep("NS", 7), rep("S", 7))
x <- aldex.clr(selex, conds, mc.samples = 2, denom = "iqlr", verbose = FALSE)
Denom <- getDenom(x)

# to find the names of housekeeping genes used
getFeatureNames(x)[getDenom(x)]