examples/pls-example.R

In ajabadi/mixOmics2: Omics Data Integration Project

#' \dontrun{
library(mixOmics.data)

## ---------------- with X and Y as matrices
X <- linnerud$exercise
Y <- linnerud$physiological
pls.res1 <- pls(X=X, Y=Y)
plotVar(pls.res1)

## ---------------- formula method for matrices
## 'formula' argument should be explicitly mentioned (formula = ...)
## for correct method dispatch
pls.res2 <- pls(formula = Y ~ X)
## exclude calls and see if all outputs  are identical
identical(pls.res1[-1], pls.res2[-1])
#> TRUE
## ---------------- MultiAssayExperiment and assay names as X and Y
## 'data' argument should be explicitly mentioned for correct method dispatch
pls.res3 <- pls(X='exercise', Y='physiological', data = linnerud.mae)
identical(pls.res1[-1], pls.res3[-1])
#> TRUE

## ---------------- MultiAssayExperiment and formula with assay names
pls.res4 <- pls(formula = physiological ~ exercise, data = linnerud.mae, mode = "classic",)
identical(pls.res1[-1], pls.res4[-1])
#> TRUE

## ---------------- MultiAssayExperiment; X=assay and Y=colData
toxicity.pls1 <- pls(data = liver.toxicity.mae,  formula = Dose.Group~gene, ncomp = 3)
toxicity.pls2 <- pls(data = liver.toxicity.mae,  Y='Dose.Group', X='gene', ncomp = 3)
identical(toxicity.pls1[-1], toxicity.pls2[-1])
#> TRUE

#' }