getDenom {ALDEx2}R Documentation

getDenom

Description

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

Usage

getDenom(.object)

Arguments

.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.

Details

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

Value

A vector of values.

See Also

aldex.clr

Examples

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)]
[Package ALDEx2 version 1.14.1 Index]