calc_freq

C++ Function Reference

1 Signature

double BigDataStatMeth::calc_freq(Rcpp::NumericVector x)

2 Description

Calculates the Minor Allele Frequency (MAF) from binary genotype data.

3 Parameters

x (Rcpp::NumericVector): NumericVector containing binary genotype data (0/1 encoded)

4 Returns

double MAF value between 0 and 0.5

5 Details

xNumericVector containing binary genotype data (0/1 encoded) double MAF value between 0 and 0.5 This function calculates MAF for a vector of binary genotypes:Counts occurrences of reference (0) and alternate (1) allelesCalculates frequency as (n0 + 0.5*n1)/total_lengthEnsures MAF is ≤ 0.5 by taking complement if necessary

6 Call Graph

7 Source Code

Implementation

File: inst/include/hdf5Omics/hdf5OmicsUtils.hpp • Lines 61-79

inline double calc_freq(Rcpp::NumericVector x)
    {
        
        int len = x.size();
        
        std::vector<double> xc = Rcpp::as<std::vector<double> >(x);
        
        int n0 = std::count (xc.begin(), xc.end(), 0);
        int n1 = std::count (xc.begin(), xc.end(), 1);
        
        double maf = (double(n0)/len) + 0.5*(double(n1)/len);
        
        if( maf > 0.5 ) { 
            maf = 1 - maf;
        }
        
        return maf;
        
    }

8 Usage Example

#include "BigDataStatMeth.hpp"

// Example usage
auto result = calc_freq(...);

---
title: "calc_freq"
subtitle: "C++ Function Reference"
---

## Signature

```cpp
double BigDataStatMeth::calc_freq(Rcpp::NumericVector x)
```

## Description

Calculates the Minor Allele Frequency (MAF) from binary genotype data.

## Parameters

- `x` (`Rcpp::NumericVector`): NumericVector containing binary genotype data (0/1 encoded)

## Returns

double MAF value between 0 and 0.5

## Details

xNumericVector containing binary genotype data (0/1 encoded) double MAF value between 0 and 0.5
This function calculates MAF for a vector of binary genotypes:Counts occurrences of reference (0) and alternate (1) allelesCalculates frequency as (n0 + 0.5*n1)/total_lengthEnsures MAF is ≤ 0.5 by taking complement if necessary

## Call Graph

::: {.diagram-section}
<object type="image/svg+xml" data="images/namespace_big_data_stat_meth_a03a8786966faa491d4f359d52ea059e4_cgraph.svg" class="class-diagram">
  <img src="images/namespace_big_data_stat_meth_a03a8786966faa491d4f359d52ea059e4_cgraph.svg" alt="Function dependencies"/>
</object>
:::

## Source Code

::: {.callout-note collapse="true"}
### Implementation

**File:** `inst/include/hdf5Omics/hdf5OmicsUtils.hpp` • **Lines 61-79**

```cpp
inline double calc_freq(Rcpp::NumericVector x)
    {
        
        int len = x.size();
        
        std::vector<double> xc = Rcpp::as<std::vector<double> >(x);
        
        int n0 = std::count (xc.begin(), xc.end(), 0);
        int n1 = std::count (xc.begin(), xc.end(), 1);
        
        double maf = (double(n0)/len) + 0.5*(double(n1)/len);
        
        if( maf > 0.5 ) { 
            maf = 1 - maf;
        }
        
        return maf;
        
    }
```
:::

## Usage Example

```cpp
#include "BigDataStatMeth.hpp"

// Example usage
auto result = calc_freq(...);
```