filter_low_coverage

filter_low_coverage

OMICS

1 Description

Removes columns (SNPs) or rows (samples) whose proportion of missing values (NAs) exceeds pcent. Writes result to a new dataset.

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

2 Usage

filter_low_coverage(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 + .
`pcent`	Numeric in [0,1]. Maximum allowed NA proportion (default ). Features above this are removed.
`by_cols`	Logical. Filter columns (, default) or rows.
`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, NA), 200, replace = TRUE,
                       prob = c(.25, .25, .25, .25)), 20, 10)
X   <- hdf5_create_matrix(fn, "geno/raw", data = snps)

# Filter with auto output path (adds "_filtered" suffix)
out <- filter_low_coverage(X, pcent = 0.1)

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

---
title: "filter_low_coverage"
subtitle: "filter_low_coverage"
---

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

## Description

Removes columns (SNPs) or rows (samples) whose proportion of missing values
(NAs) exceeds `pcent`. Writes result to a new dataset.

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

## Usage

```r
filter_low_coverage(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{"_filtered"}. |
| `pcent` | Numeric in \[0,1\]. Maximum allowed NA proportion   (default \code{0.05}). Features above this are removed. |
| `by_cols` | Logical. Filter columns (\code{TRUE}, default) or rows. |
| `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, NA), 200, replace = TRUE,
                       prob = c(.25, .25, .25, .25)), 20, 10)
X   <- hdf5_create_matrix(fn, "geno/raw", data = snps)

# Filter with auto output path (adds "_filtered" suffix)
out <- filter_low_coverage(X, pcent = 0.1)

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

```