com.github.jessemull.microflexinteger.stat

Class Percentile

java.lang.Object

com.github.jessemull.microflexinteger.stat.Percentile

public class Percentile
extends Object

This class calculates percentiles for integer plate stacks, plates, wells and well sets using the following steps:

1. Calculate R as P/100 x (N + 1) where N is the number of values and P is the desired percentile
2. Define IR as the integer portion of R
3. Define FR as the fractional portion of R
4. Find the scores with Rank IR and with Rank IR + 1
5. Interpolate using the formula (Score IR+1 - Score IR) * FR + Score IR and return the result

Statistical operations can be performed on stacks, plates, sets and wells using standard or aggregated functions. Standard functions calculate the desired statistic for each well in the stack, plate or set. Aggregated functions aggregate the values from all the wells in the stack, plate or set and perform the statistical operation on the aggregated values. Both standard and aggregated functions can be performed on a subset of data within the stack, plate, set or well.

The methods within the MicroFlex library are meant to be flexible and the descriptive statistic object supports operations using a single stack, plate, set or well as well as collections and arrays of stacks, plates, sets or wells.

Operation	Beginning Index	Length of Subset	Input/Output
Standard	+/-	+/-	Accepts a single well, set, plate or stack as input Calculates the statistic for each well in a well, set, plate or stack
Aggregated	+/-	+/-	Accepts a single well/set/plate/stack or a collection/array of wells/sets/plates/stacks as input Aggregates the data from all the wells in a well/set/plate/stack and calculates the statistic using the aggregated data

Author:

Jesse L. Mull

Constructor Summary

Constructors

Constructor and Description
Percentile()

Method Summary

Modifier and Type	Method and Description
double	calculate(List<Double> list, int p) Calculates the percentile.
double	calculate(List<Double> list, int begin, int length, int p) Calculates the percentile of the values between the beginning and ending indices.
Map<Well,Double>	plate(Plate plate, int p) Returns the percentile for each plate well.
Map<Well,Double>	plate(Plate plate, int begin, int length, int p) Returns the percentile for each plate well using the values between the beginning and ending indices.
Map<Plate,Double>	platesAggregated(Collection<Plate> collection, int p) Returns the aggregated percentile for each plate.
Map<Plate,Double>	platesAggregated(Collection<Plate> collection, int begin, int length, int p) Returns the aggregated percentile for each plate using the values between the indices.
Map<Plate,Double>	platesAggregated(Plate[] array, int p) Returns the aggregated percentile for each plate.
Map<Plate,Double>	platesAggregated(Plate[] array, int begin, int length, int p) Returns the aggregated percentile for each plate using the values between the indices.
double	platesAggregated(Plate plate, int p) Returns the aggregated percentile for the plate.
double	platesAggregated(Plate plate, int begin, int length, int p) Returns the aggregated percentile for each plate using the values between the indices.
Map<Well,Double>	set(WellSet set, int p) Returns the percentile of each well in the well set.
Map<Well,Double>	set(WellSet set, int begin, int length, int p) Returns the percentile of each well in the well set using the values between the beginning and ending indices.
Map<WellSet,Double>	setsAggregated(Collection<WellSet> collection, int p) Returns the aggregated percentile for each well set.
Map<WellSet,Double>	setsAggregated(Collection<WellSet> collection, int begin, int length, int p) Returns the aggregated percentile for each well set using the values between the indices.
Map<WellSet,Double>	setsAggregated(WellSet[] array, int p) Returns the aggregated percentile for each well set.
Map<WellSet,Double>	setsAggregated(WellSet[] array, int begin, int length, int p) Returns the aggregated percentile for each well set using the values between the indices.
double	setsAggregated(WellSet set, int p) Returns the aggregated percentile for the well set.
double	setsAggregated(WellSet set, int begin, int length, int p) Returns the aggregated percentile for each well set using the values between the indices.
double	well(Well well, int p) Returns the well percentile.
double	well(Well well, int begin, int length, int p) Returns the well percentile for the values between the beginning and ending indices.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Percentile

public Percentile()

Method Detail

plate

public Map<Well,Double> plate(Plate plate,
                              int p)

Returns the percentile for each plate well.

Parameters:

Plate - the plate

int - the percentile

Returns:

map of wells and results

plate

public Map<Well,Double> plate(Plate plate,
                              int begin,
                              int length,
                              int p)

Returns the percentile for each plate well using the values between the beginning and ending indices.

Parameters:

Plate - the plate

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of wells and results

platesAggregated

public double platesAggregated(Plate plate,
                               int p)

Returns the aggregated percentile for the plate.

Parameters:

Plate - the plate

int - the percentile

Returns:

the aggregated result

platesAggregated

public Map<Plate,Double> platesAggregated(Collection<Plate> collection,
                                          int p)

Returns the aggregated percentile for each plate.

Parameters:

Collection - collection of plates

int - the percentile

Returns:

map of plates and aggregated results

platesAggregated

public Map<Plate,Double> platesAggregated(Plate[] array,
                                          int p)

Returns the aggregated percentile for each plate.

Parameters:

PlateInteger[] - array of plates

int - the percentile

Returns:

map of plates and aggregated result

platesAggregated

public double platesAggregated(Plate plate,
                               int begin,
                               int length,
                               int p)

Returns the aggregated percentile for each plate using the values between the indices.

Parameters:

Plate - the plate

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

the aggregated result

platesAggregated

public Map<Plate,Double> platesAggregated(Collection<Plate> collection,
                                          int begin,
                                          int length,
                                          int p)

Returns the aggregated percentile for each plate using the values between the indices.

Parameters:

Collection - collection of plates

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of plates and aggregated results

platesAggregated

public Map<Plate,Double> platesAggregated(Plate[] array,
                                          int begin,
                                          int length,
                                          int p)

Returns the aggregated percentile for each plate using the values between the indices.

Parameters:

PlateInteger[] - array of plates

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of plates and aggregated results

set

public Map<Well,Double> set(WellSet set,
                            int p)

Returns the percentile of each well in the well set.

Parameters:

WellSet - the well set

int - the percentile

Returns:

map of wells and results

set

public Map<Well,Double> set(WellSet set,
                            int begin,
                            int length,
                            int p)

Returns the percentile of each well in the well set using the values between the beginning and ending indices.

Parameters:

WellSet - the well set

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of wells and results

setsAggregated

public double setsAggregated(WellSet set,
                             int p)

Returns the aggregated percentile for the well set.

Parameters:

WellSet - the well set

int - the percentile

Returns:

the aggregated result

setsAggregated

public Map<WellSet,Double> setsAggregated(Collection<WellSet> collection,
                                          int p)

Returns the aggregated percentile for each well set.

Parameters:

Collection - collection of well sets

int - the percentile

Returns:

map of well sets and aggregated results

setsAggregated

public Map<WellSet,Double> setsAggregated(WellSet[] array,
                                          int p)

Returns the aggregated percentile for each well set.

Parameters:

WellSetInteger[] - array of well sets

int - the percentile

Returns:

map of well sets and aggregated results

setsAggregated

public double setsAggregated(WellSet set,
                             int begin,
                             int length,
                             int p)

Returns the aggregated percentile for each well set using the values between the indices.

Parameters:

WellSet - the well set

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

the aggregated result

setsAggregated

public Map<WellSet,Double> setsAggregated(Collection<WellSet> collection,
                                          int begin,
                                          int length,
                                          int p)

Returns the aggregated percentile for each well set using the values between the indices.

Parameters:

Collection - collection of well sets

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of well sets and aggregated results

setsAggregated

public Map<WellSet,Double> setsAggregated(WellSet[] array,
                                          int begin,
                                          int length,
                                          int p)

Returns the aggregated percentile for each well set using the values between the indices.

Parameters:

WellSetInteger[] - array of well sets

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

map of well sets and aggregated results

well

public double well(Well well,
                   int p)

Returns the well percentile.

Parameters:

Well - the well

int - the percentile

Returns:

the result

well

public double well(Well well,
                   int begin,
                   int length,
                   int p)

Returns the well percentile for the values between the beginning and ending indices.

Parameters:

Well - the well

int - beginning index of subset

int - length of the subset

int - the percentile

Returns:

the result

calculate

public double calculate(List<Double> list,
                        int p)

Calculates the percentile.

Parameters:

List - the list

int - the percentile

Returns:

the result

calculate

public double calculate(List<Double> list,
                        int begin,
                        int length,
                        int p)

Calculates the percentile of the values between the beginning and ending indices.

Parameters:

List - the list

int - beginning index of subset

int - length of subset

int - the percentile

Returns:

the result