sweep.HDF5Matrix

sweep.HDF5Matrix

OTHER

1 Description

S3 method of base::sweep() for HDF5Matrix objects. Broadcasts a 1-row HDF5Matrix (acting as the STATS vector) across every row or column of the matrix, element-wise.

2 Usage

sweep.HDF5Matrix(...)

3 Arguments

Parameter	Description
`x`	An (the matrix to sweep over).
`MARGIN`	Integer. (default, sweep over columns) or (sweep over rows). Corresponds to : means .
`STATS`	An with one row or one column (the vector to broadcast). Must be in the same HDF5 file as .
`FUN`	Character. Operation: , , (default), , .
`check.margin`	Ignored (kept for S3 signature compatibility).
`paral`	Logical or NULL.
`threads`	Integer or NULL.
`compression`	Integer (0-9) or NULL.

4 Value

A new .

5 Examples

\donttest{
fn <- tempfile(fileext = ".h5")

mat <- matrix(rnorm(100), 10, 10)
X   <- hdf5_create_matrix(fn, "data/X", data = mat)

# STATS must be an HDF5Matrix with one row or one column
# Create a 1-row vector with column means
col_means_vec <- colMeans(as.matrix(X))
stats_hdf5    <- hdf5_create_matrix(fn, "data/col_means",
                                     data = matrix(col_means_vec, 1, 10))

# Column-center X (MARGIN = 2)
X_c <- sweep(X, 2, stats_hdf5, "-")

# Verify first column is centered
all.equal(as.matrix(X_c)[, 1],
          mat[, 1] - col_means_vec[1])

hdf5_close_all()
unlink(fn)
}

---
title: "sweep.HDF5Matrix"
subtitle: "sweep.HDF5Matrix"
---

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

## Description

S3 method of `base::sweep()` for `HDF5Matrix` objects.
Broadcasts a 1-row `HDF5Matrix` (acting as the STATS vector)
across every row or column of the matrix, element-wise.

## Usage

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

::: {.param-table}
| Parameter | Description |
|-----------|-------------|
| `x` | An \code{HDF5Matrix} (the matrix to sweep over). |
| `MARGIN` | Integer. \code{2} (default, sweep over columns) or   \code{1} (sweep over rows). Corresponds to \code{byrows}:   \code{MARGIN = 1} means \code{byrows = TRUE}. |
| `STATS` | An \code{HDF5Matrix} with one row or one column   (the vector to broadcast). Must be in the same HDF5 file as \code{x}. |
| `FUN` | Character. Operation: \code{"+"}, \code{"-"},   \code{"*"} (default), \code{"/"}, \code{"pow"}. |
| `check.margin` | Ignored (kept for S3 signature compatibility). |
| `paral` | Logical or NULL. |
| `threads` | Integer or NULL. |
| `compression` | Integer (0-9) or NULL. |
:::

## Value

::: {.return-value}
A new \code{HDF5Matrix}.

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

\donttest{
fn <- tempfile(fileext = ".h5")

mat <- matrix(rnorm(100), 10, 10)
X   <- hdf5_create_matrix(fn, "data/X", data = mat)

# STATS must be an HDF5Matrix with one row or one column
# Create a 1-row vector with column means
col_means_vec <- colMeans(as.matrix(X))
stats_hdf5    <- hdf5_create_matrix(fn, "data/col_means",
                                     data = matrix(col_means_vec, 1, 10))

# Column-center X (MARGIN = 2)
X_c <- sweep(X, 2, stats_hdf5, "-")

# Verify first column is centered
all.equal(as.matrix(X_c)[, 1],
          mat[, 1] - col_means_vec[1])

hdf5_close_all()
unlink(fn)
}

```