getReads-method: getReads

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

getReads

Description

Returns the count table used as input for analysis, for aldex.clr object. Note this count table has features that are 0 in all samples removed, and a uniform prior of 0.5 is applied.

Usage

  getReads(.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 the count table.Note this count table has features that are 0 in all samples removed, and a uniform prior of 0.5 is applied.

Value

A data frame representing the count table used as input for analysis.

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)
reads <- getReads(x)

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