filter_maf

filter_maf

OMICS

1 Description

Removes columns or rows whose Minor Allele Frequency (MAF) exceeds maf_threshold. Designed for 0/1/2-coded diploid genotype matrices.

When out_group/out_dataset are NULL (default) the result is written alongside the input dataset with suffix "_maf_filtered".

2 Usage

filter_maf(x, ...)

3 Arguments

Parameter	Description
`x`	An containing SNP data.
`out_group`	Output group. (default) = same group as input.
`out_dataset`	Output dataset name. (default) = input name + .
`maf_threshold`	Numeric in [0, 0.5]. MAF threshold (default ). SNPs with MAF above this value are removed.
`by_cols`	Logical. Process by columns (, default) or rows.
`block_size`	Integer. Block size for I/O. Default .
`overwrite`	Logical. Overwrite existing output. Default .

4 Value

pointing to the filtered dataset.

5 Examples

\donttest{
fn <- tempfile(fileext = ".h5")
snps <- matrix(sample(c(0, 1, 2), 200, replace = TRUE,
                       prob = c(.6, .3, .1)), 20, 10)
X   <- hdf5_create_matrix(fn, "geno/raw", data = snps)

# Filter with auto output path (adds "_maf_filtered" suffix)
out <- filter_maf(X, maf_threshold = 0.05)

# Filter with explicit output
out2 <- filter_maf(X, out_group = "geno",
                   out_dataset = "maf_filtered", overwrite = TRUE)
hdf5_close_all()
unlink(fn)
}

---
title: "filter_maf"
subtitle: "filter_maf"
---

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

## Description

Removes columns or rows whose Minor Allele Frequency (MAF) exceeds
`maf_threshold`. Designed for 0/1/2-coded diploid genotype matrices.

When `out_group`/`out_dataset` are `NULL` (default) the
result is written alongside the input dataset with suffix `"_maf_filtered"`.

## Usage

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

::: {.param-table}
| Parameter | Description |
|-----------|-------------|
| `x` | An \code{HDF5Matrix} containing SNP data. |
| `out_group` | Output group. \code{NULL} (default) = same group as input. |
| `out_dataset` | Output dataset name. \code{NULL} (default) = input name + \code{"_maf_filtered"}. |
| `maf_threshold` | Numeric in \[0, 0.5\]. MAF threshold (default \code{0.05}).   SNPs with MAF **above** this value are removed. |
| `by_cols` | Logical. Process by columns (\code{FALSE}, default) or rows. |
| `block_size` | Integer. Block size for I/O. Default \code{100L}. |
| `overwrite` | Logical. Overwrite existing output. Default \code{FALSE}. |
:::

## Value

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

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

\donttest{
fn <- tempfile(fileext = ".h5")
snps <- matrix(sample(c(0, 1, 2), 200, replace = TRUE,
                       prob = c(.6, .3, .1)), 20, 10)
X   <- hdf5_create_matrix(fn, "geno/raw", data = snps)

# Filter with auto output path (adds "_maf_filtered" suffix)
out <- filter_maf(X, maf_threshold = 0.05)

# Filter with explicit output
out2 <- filter_maf(X, out_group = "geno",
                   out_dataset = "maf_filtered", overwrite = TRUE)
hdf5_close_all()
unlink(fn)
}

```