getScaleSamples-method: getScaleSamples

In ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

getScaleSamples

Description

Returns the log2 scale samples if scale simulation is used, for aldex.clr object.

Usage

  getScaleSamples(.object)

Arguments

.object

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

Details

Returns NULL if scale simulation was not used or a matrix of log2 scale samples if scale simuation was used.

Value

A matrix representing the log2 scale samples if scale simulation was used.

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 = "all", verbose = FALSE)
scale.samps <- getScaleSamples(x)

ggloor/ALDEx_bioc documentation built on Oct. 31, 2023, 1:13 a.m.