BasicMathFunctions (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.math.BasicMathFunctions

```
public class BasicMathFunctions
extends Object
```
Class used to perform basic mathematical functions.

Author:

Marc Vaudel

Constructor Summary

Constructors
Constructor and Description

BasicMathFunctions()

Constructors
Constructor and Description
`BasicMathFunctions()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static Long`	`factorial(Integer n)` Returns n! as a long.
`static Long`	`factorial(Integer n, Integer k)` Returns n!/k!, null if it cannot fit in a long.
`static Long`	`getCombination(int k, int n)` Returns the number of k-combinations in a set of n elements.
`static double`	`getCorrelation(ArrayList<Double> series1, ArrayList<Double> series2)` Returns the population Pearson correlation r between series1 and series2.
`static double`	`getRobustCorrelation(ArrayList<Double> series1, ArrayList<Double> series2)` Returns the population Pearson correlation r between series1 and series2.
`static double`	`log(double input, double base)` Returns the log of the input in the desired base.
`static double`	`mad(ArrayList<Double> ratios)` Method estimating the median absolute deviation.
`static double`	`mad(double[] ratios)` Method estimating the median absolute deviation.
`static double`	`mean(ArrayList<Double> input)` Convenience method returning the mean of a list of doubles.
`static double`	`median(ArrayList<Double> input)` Method to estimate the median.
`static double`	`median(double[] ratios)` Method to estimate the median.
`static double`	`medianSorted(ArrayList<Double> input)` Method to estimate the median of a sorted list.
`static double`	`percentile(ArrayList<Double> input, double percentile)` Returns the desired percentile in a given list of double.
`static double`	`percentile(double[] input, double percentile)` Returns the desired percentile in a given array of double.
`static double`	`percentileSorted(ArrayList<Double> input, double percentile)` Returns the desired percentile in a given list of double.
`static double`	`std(ArrayList<Double> input)` Convenience method returning the standard deviation of a list of doubles.
`static double`	`sum(ArrayList<Double> input)` Convenience method returning the sum of a list of doubles.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BasicMathFunctions
```
public BasicMathFunctions()
```
- Method Detail
  - factorial
```
public static Long factorial(Integer n)
```
    Returns n! as a long. Returns null if the capacity of a long is not sufficient (ie n higher than 20).
    
    Parameters:
    
    n - a given integer
    
    Returns:
    
    the corresponding factorial
  - factorial
```
public static Long factorial(Integer n,
                             Integer k)
```
    Returns n!/k!, null if it cannot fit in a long.
    
    Parameters:
    
    n - a given integer
    
    k - a given integer
    
    Returns:
    
    the corresponding factorial
  - getCombination
```
public static Long getCombination(int k,
                                  int n)
```
    Returns the number of k-combinations in a set of n elements. If n!/k! cannot fit in a long, null is returned, use BigDecimal instead (see BigFunctions).
    
    Parameters:
    
    k - the number of k-combinations
    
    n - the number of elements
    
    Returns:
    
    the number of k-combinations in a set of n elements
  - median
```
public static double median(double[] ratios)
```
    Method to estimate the median.
    
    Parameters:
    
    ratios - array of double
    
    Returns:
    
    median of the input
  - median
```
public static double median(ArrayList<Double> input)
```
    Method to estimate the median.
    
    Parameters:
    
    input - ArrayList of double
    
    Returns:
    
    median of the input
  - medianSorted
```
public static double medianSorted(ArrayList<Double> input)
```
    Method to estimate the median of a sorted list.
    
    Parameters:
    
    input - ArrayList of double
    
    Returns:
    
    median of the input
  - percentile
```
public static double percentile(double[] input,
                                double percentile)
```
    Returns the desired percentile in a given array of double. If the percentile is between two values a linear interpolation is done.
    
    Parameters:
    
    input - the input array
    
    percentile - the desired percentile. 0.01 returns the first percentile. 0.5 returns the median.
    
    Returns:
    
    the desired percentile
  - percentile
```
public static double percentile(ArrayList<Double> input,
                                double percentile)
```
    Returns the desired percentile in a given list of double. If the percentile is between two values a linear interpolation is done. Note: When calculating multiple percentiles on the same list, it is advised to sort it and use percentileSorted.
    
    Parameters:
    
    input - the input list
    
    percentile - the desired percentile. 0.01 returns the first percentile. 0.5 returns the median.
    
    Returns:
    
    the desired percentile
  - percentileSorted
```
public static double percentileSorted(ArrayList<Double> input,
                                      double percentile)
```
    Returns the desired percentile in a given list of double. If the percentile is between two values a linear interpolation is done. The list must be sorted prior to submission.
    
    Parameters:
    
    input - the input list
    
    percentile - the desired percentile. 0.01 returns the first percentile. 0.5 returns the median.
    
    Returns:
    
    the desired percentile
  - mad
```
public static double mad(double[] ratios)
```
    Method estimating the median absolute deviation.
    
    Parameters:
    
    ratios - array of doubles
    
    Returns:
    
    the mad of the input
  - mad
```
public static double mad(ArrayList<Double> ratios)
```
    Method estimating the median absolute deviation.
    
    Parameters:
    
    ratios - array of doubles
    
    Returns:
    
    the mad of the input
  - log
```
public static double log(double input,
                         double base)
```
    Returns the log of the input in the desired base.
    
    Parameters:
    
    input - the input
    
    base - the log base
    
    Returns:
    
    the log value of the input in the desired base.
  - std
```
public static double std(ArrayList<Double> input)
```
    Convenience method returning the standard deviation of a list of doubles. Returns 0 if the list is null or of size < 2.
    
    Parameters:
    
    input - input list
    
    Returns:
    
    the corresponding standard deviation
  - mean
```
public static double mean(ArrayList<Double> input)
```
    Convenience method returning the mean of a list of doubles.
    
    Parameters:
    
    input - input list
    
    Returns:
    
    the corresponding mean
  - sum
```
public static double sum(ArrayList<Double> input)
```
    Convenience method returning the sum of a list of doubles.
    
    Parameters:
    
    input - input list
    
    Returns:
    
    the corresponding mean
  - getCorrelation
```
public static double getCorrelation(ArrayList<Double> series1,
                                    ArrayList<Double> series2)
```
    Returns the population Pearson correlation r between series1 and series2.
    
    Parameters:
    
    series1 - first series to compare
    
    series2 - second series to compare
    
    Returns:
    
    the Pearson correlation factor
  - getRobustCorrelation
```
public static double getRobustCorrelation(ArrayList<Double> series1,
                                          ArrayList<Double> series2)
```
    Returns the population Pearson correlation r between series1 and series2. Here the correlation factor is estimated using median and percentile distance instead of mean and standard deviation.
    
    Parameters:
    
    series1 - the first series to inspect
    
    series2 - the second series to inspect
    
    Returns:
    
    a robust version of the Pearson correlation factor

Class BasicMathFunctions

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicMathFunctions

Method Detail

factorial

factorial

getCombination

median

median

medianSorted

percentile

percentile

percentileSorted

mad

mad

log

std

mean

sum

getCorrelation

getRobustCorrelation