In ajabadi/mixOmics2: Omics Data Integration Project

library(knitr)
opts_chunk$set( echo = TRUE, eval = FALSE, warning = FALSE, fig.path = './images/', fig.asp = 1, out.width = "50%", cache = FALSE)
opts_knit$set(root.dir = "./images/", cache.path = "./images/")

News

• August 2019: pls family functions now support MultiAssayExperiment and formula classes as input. check out example.
• July 2019: pca family functions now support MultiAssayExperiment data. see example.

PLS family now supports MultiAssayExperiment and formula classes {#pls-mae-formula}

suppressMessages({library(mixOmics2); library(mixOmics.data)})

## with X and Y as matrices
X <- linnerud$exercise
Y <- linnerud$physiological

pls.res_XY <- pls(X = X, Y = Y)
pls.res_fm <- pls(formula = Y ~ X)
pls.res_fm_MAE <- pls(data = linnerud.mae, formula = physiological~exercise)
## same output for all three
identical(pls.res_XY[-1], pls.res_fm[-1])
identical(pls.res_XY[-1], pls.res_fm_MAE[-1])
plotVar(pls.res_fm)

See examples/pls.R, examples/spls.R, examples/splsda.R,... for more.

PCA family now supports MultiAssayExperiment data {#pca-mae}

suppressMessages({library(mixOmics2); library(mixOmics.data)})

## example with MultiAssayExperiment class
pca.res <- pca(X = multidrug.mae, assay = 'ABC.trans', ncomp = 4, scale = TRUE)
plotIndiv(pca.res, ind.names = multidrug$cell.line$Class,
          group = as.numeric(as.factor(multidrug$cell.line$Class)))

See examples/pca.R, examples/spca.R, ... for more.

ajabadi/mixOmics2 documentation built on Aug. 9, 2019, 1:08 a.m.