lasso {MetNet} | R Documentation

## Create a adjacency matrix based on LASSO

### Description

`lasso` infers a adjacency matrix using LASSO using the `stabsel.matrix` function from the `stabs` package. `lasso` extracts the predictors from the function `stabsel.matrix` and writes the presence/absence of this connection to a matrix that is returned.

### Usage

    lasso(x, parallel=FALSE, ...)

### Arguments

`x` | matrix, where columns are the samples and the rows are features (metabolites), cell entries are intensity values
`parallel` | logical, should computation be parallelized? If `parallel=TRUE` the `bplapply` will be applied if `parallel=FALSE` the `lapply` function will be applied.
`...` | parameters passed to `stabsel.matrix`

### Details

For use of the parameters used in the `stabsel.matrix` function, refer to ?stabs::stabsel.matrix.

### Value

matrix, matrix with edges inferred from LASSO algorithm `stabsel.matrix`

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### Examples

    data("x_test", package="MetNet")
    x <- x_test[, 3:dim(x_test)[2]]
    x <- as.matrix(x)
    x_z <- t(apply(x, 1, function(y) (y - mean(y)) / sd(y)))
    ## Not run: lasso(x_z, PFER=0.75, cutoff=0.95)

[Package MetNet version 1.0.1 Index]