aldex.corr {ALDEx2}R Documentation

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. By default uses pearson but method="kendall" or "spearman" can be passed to the cor.test function.

Usage

aldex.corr(clr, cont.var, verbose = FALSE, ...)

Arguments

clr

An ALDEx2 object. The output of aldex.clr.

cont.var

A continuous numeric vector

verbose

A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets. Applies to effect = TRUE.

...

Arguments passed to cor.test.

Value

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

Author(s)

Thom Quinn, Greg Gloor

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[1201:1600,]
conds <- c(rep("N", 7), rep("S",7))
cont.var <-  1:14
x <- aldex.clr(selex, conds)
corr.test <- aldex.corr(x, cont.var)

[Package ALDEx2 version 1.18.0 Index]