scale.HDF5Matrix

scale.HDF5Matrix

OTHER

1 Usage

scale.HDF5Matrix(...)

2 Arguments

Parameter	Description
`x`	An object.
`center`	Logical (or numeric vector, see Details). If (default) subtract column means before scaling.
`scale`	Logical (or numeric vector, see Details). If (default) divide by column standard deviations.
`byrows`	Logical. If normalize row-wise instead of column-wise. Default .
`wsize`	Integer or NULL. Block size for HDF5 reads (NULL = auto).
`result_path`	Output location. (default) writes to in the same file. A character string writes to that path in the same file. A named list writes to a different file.
`compression`	Integer (0-9) or NULL. gzip compression level for the result datasets. NULL uses the global option set by (default 6). Use to disable compression (faster for benchmarks).

3 Value

An pointing to the normalized dataset on disk.

4 Details

Passing a pre-computed numeric vector as center or scale is not currently supported. If a vector is supplied it is coerced to a logical (TRUE if length(x) > 0) and a warning is issued.

The returned HDF5Matrix carries scaled:center and scaled:scale attributes (numeric vectors), mirroring the behavior of base::scale().

5 Examples

\donttest{
tmp <- tempfile(fileext = ".h5")
X   <- hdf5_create_matrix(tmp, "data/M",
                           data = matrix(rnorm(500), 50, 10))
Xs  <- scale(X)                         # center=TRUE, scale=TRUE by cols
cat("scaled:center[1]:", attr(Xs, "scaled:center")[1], "\n")
X$close(); Xs$close(); unlink(tmp)
}

---
title: "scale.HDF5Matrix"
subtitle: "scale.HDF5Matrix"
---

<span class="category-badge other">OTHER</span>

## Usage

```r
scale.HDF5Matrix(...)
```
## Arguments

::: {.param-table}
| Parameter | Description |
|-----------|-------------|
| `x` | An \code{HDF5Matrix} object. |
| `center` | Logical (or numeric vector, see Details).  If \code{TRUE}                    (default) subtract column means before scaling. |
| `scale` | Logical (or numeric vector, see Details).  If \code{TRUE}                    (default) divide by column standard deviations. |
| `byrows` | Logical.  If \code{TRUE} normalize row-wise instead of                    column-wise. Default \code{FALSE}. |
| `wsize` | Integer or NULL.  Block size for HDF5 reads (NULL = auto). |
| `result_path` | Output location.  \code{NULL} (default) writes to                    \code{"NORMALIZED/<group>/<dataset>"} in the same file.                    A character string writes to that path in the same file.                    A named list \code{list(file=, path=)} writes to a                    different file. |
| `compression` | Integer (0-9) or NULL. gzip compression level for the   result datasets.  NULL uses the global option set by   \code{\link{hdf5matrix_options}} (default 6).  Use \code{0} to disable   compression (faster for benchmarks). |
:::

## Value

::: {.return-value}
An \code{HDF5Matrix} pointing to the normalized dataset on disk.

:::
## Details

Passing a pre-computed numeric vector as `center` or `scale` is
not currently supported.  If a vector is supplied it is coerced to a logical
(`TRUE` if `length(x) > 0`) and a warning is issued.

The returned `HDF5Matrix` carries `scaled:center` and
`scaled:scale` attributes (numeric vectors), mirroring the behavior of
`base::scale()`.

## Examples
```{r}
#| eval: false
#| warning: false

\donttest{
tmp <- tempfile(fileext = ".h5")
X   <- hdf5_create_matrix(tmp, "data/M",
                           data = matrix(rnorm(500), 50, 10))
Xs  <- scale(X)                         # center=TRUE, scale=TRUE by cols
cat("scaled:center[1]:", attr(Xs, "scaled:center")[1], "\n")
X$close(); Xs$close(); unlink(tmp)
}

```