getDenom-method: getDenom

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

getDenom

Description

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

Usage

  getDenom(.object)

Arguments

.object

A aldex.clr object.

Details

Returns the offset of the features used as the denominator as the basis for the log-ratio. A vector of numbers is the offset of the non-0 features used in the denominator.

Value

A vector of integer row offsets.

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)]

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