aldex.corr: Calculate correlation with a continuous variable

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

Calculate correlation with a continuous variable

Description

aldex.corr calculates the expected values for the correlation between each feature and a continuous variable, using data returned returned by aldex.clr and a vector of the continuous variable. Returns results of Pearson, Spearman and Kendall tests.

Usage

aldex.corr(clr, cont.var)

Arguments

clr	An ALDEx2 object. The output of aldex.clr.
cont.var	A continuous numeric vector

Value

Returns a data.frame of the average Pearson, Spearman and Kendall coefficients and their p-values for each feature, with FDR appended as a BH column.

Author(s)

Arianne Albert, Greg Gloor, Thom Quinn

References

Please use the citation given by citation(package="ALDEx2").

See Also

aldex, aldex.clr, aldex.ttest, aldex.kw, aldex.glm, aldex.effect, aldex.corr, selex

Examples

data(selex)
#subset for efficiency
selex <- selex[1:50,]
conds <- c(rep("N", 7), rep("S",7))
cont.var <-  c(rep(1,7), rep(2,7))
x <- aldex.clr(selex, conds, mc.samples=16)
corr.test <- aldex.corr(x, cont.var)

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