Omics QC & Preprocessing

1 Overview

Omics-specific quality control: imputation of missing SNP values, filtering by missingness rate, and filtering by Minor Allele Frequency.

2 Functions

2.1 impute_snps

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.

2.2 filter_low_coverage

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

When / are (default) the result is written alongside the input dataset with the suffix .

2.3 filter_maf

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

When / are (default) the result is written alongside the input dataset with suffix .

---
title: "Omics QC & Preprocessing"
---

## Overview

Omics-specific quality control: imputation of missing SNP values, filtering by missingness rate, and filtering by Minor Allele Frequency.

## Functions


### [impute_snps](impute_snps.qmd)

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.


### [filter_low_coverage](filter_low_coverage.qmd)

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

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


### [filter_maf](filter_maf.qmd)

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

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