README.md

In ajabadi/mixOmics2: Omics Data Integration Project

This package is a developing implementation of mixOmics Bioconductor package.

The aim is to:

• implement roxygen2 documentation, and
• support MultiAssayExperiment datasets.
• support more intuitve input formats tailored to data integration such as formula class entry and support of assay names.

Installation:

The package is not complete/tested yet, but feel free to try it using:

devtools::install_github("ajabadi/mixOmics2")

You need to install the data package to be able to run the examples:

devtools::install_github("ajabadi/mixOmics.data")

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

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])

## [1] TRUE

identical(pls.res_XY[-1], pls.res_fm_MAE[-1])

## [1] TRUE

plotVar(pls.res_fm)

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

PCA family now supports MultiAssayExperiment data

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.