impute_snps

impute_snps

OMICS

1 Description

Fills NA entries in SNP data by computing column or row means of non-missing values. Intended for 0/1/2-coded diploid genotype matrices.

2 Usage

impute_snps(x, ...)

3 Arguments

Parameter	Description
`x`	An containing SNP data with NAs.
`out_group`	Output group. = same as input (default).
`out_dataset`	Output dataset name. = same as input (default, in-place).
`by_cols`	Logical. Impute by columns (, default) or rows.
`threads`	Integer. Number of threads (-1 = auto).
`overwrite`	Logical. Overwrite existing output. Default .

4 Value

pointing to the imputed dataset.

5 Examples

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

# SNP data: 0/1/2 coded, 3 = missing (not NA)
snps <- matrix(sample(c(0L, 1L, 2L, 3L), 100 * 20,
                       replace = TRUE,
                       prob    = c(0.3, 0.3, 0.3, 0.1)),
               nrow = 100, ncol = 20)

X   <- hdf5_create_matrix(tmp, "geno/raw", data = snps)
imp <- impute_snps(X, out_group = "geno", out_dataset = "imputed")
dim(imp)

hdf5_close_all()
unlink(tmp)
}

---
title: "impute_snps"
subtitle: "impute_snps"
---

<span class="category-badge omics">OMICS</span>

## Description

Fills NA entries in SNP data by computing column or row means of non-missing
values. Intended for 0/1/2-coded diploid genotype matrices.

## Usage

```r
impute_snps(x, ...)
```
## Arguments

::: {.param-table}
| Parameter | Description |
|-----------|-------------|
| `x` | An \code{HDF5Matrix} containing SNP data with NAs. |
| `out_group` | Output group. \code{NULL} = same as input (default). |
| `out_dataset` | Output dataset name. \code{NULL} = same as input (default, in-place). |
| `by_cols` | Logical. Impute by columns (\code{TRUE}, default) or rows. |
| `threads` | Integer. Number of threads (-1 = auto). |
| `overwrite` | Logical. Overwrite existing output. Default \code{FALSE}. |
:::

## Value

::: {.return-value}
\code{HDF5Matrix} pointing to the imputed dataset.

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

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

# SNP data: 0/1/2 coded, 3 = missing (not NA)
snps <- matrix(sample(c(0L, 1L, 2L, 3L), 100 * 20,
                       replace = TRUE,
                       prob    = c(0.3, 0.3, 0.3, 0.1)),
               nrow = 100, ncol = 20)

X   <- hdf5_create_matrix(tmp, "geno/raw", data = snps)
imp <- impute_snps(X, out_group = "geno", out_dataset = "imputed")
dim(imp)

hdf5_close_all()
unlink(tmp)
}

```