NEWS_of_README.Rmd

---
description: "This is a child document for README to isolate NEWS updates - see README's last chunk"
---

```{r setup-news, include=FALSE}
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

 
  * <span style="color:blue"><big>**August 2019**</big></span>: `pls` family functions now support `MultiAssayExperiment` and `formula` classes as input. [check out example](#pls-mae-formula).
  * <span style="color:blue"><big>**July 2019**</big></span>: `pca` family functions now support `MultiAssayExperiment` data. [see example](#pca-mae).

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

```{r news-pls-mae, eval=TRUE, message='hide', fig.asp=1, out.width="50%"}
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}

```{r news-pca-mae, eval=TRUE, message='hide'}
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.