data
Class Filter

java.lang.Object
  extended by data.Filter

public class Filter
extends java.lang.Object

Provides methods for filtering the values contained in a Data object

Author:
Stefanie Kaufmann

Constructor Summary
Filter()
           
 
Method Summary
static Data filter(Data data, double threshold)
          removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'
static Data filterAbsent(Data data, java.util.ArrayList<java.lang.String> label)
          Removes values that are defined as 'absent' in the attribute list Commandline option present='label'
static Data filterPQS(Data data, LinearRegression l)
          Filters data such that from each gene only one entry, the one with the lowest quality control value, is kept Commandline option pqs=min
static Data filterPQS(Data data, LinearRegression l, double threshold)
          Filters the data in such a way that all remaining entries have a quality control value lower than the given threshold Commandline option pqs='threshold'
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Filter

public Filter()
Method Detail

filter

public static Data filter(Data data,
                          double threshold)
removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'

Parameters:
data - Data object which shall be filtered
threshold - Cutoff-threshold

filterAbsent

public static Data filterAbsent(Data data,
                                java.util.ArrayList<java.lang.String> label)
Removes values that are defined as 'absent' in the attribute list Commandline option present='label'

Parameters:
data - Data object that will be filtered
label - Label name of the attribute containing the absence-information
Returns:
Filtered Data object

filterPQS

public static Data filterPQS(Data data,
                             LinearRegression l,
                             double threshold)
Filters the data in such a way that all remaining entries have a quality control value lower than the given threshold Commandline option pqs='threshold'

Parameters:
data - Data object that shall be filtered
l - Linear Regression object which correction factors will be used for filtering
threshold - A threshold which defines which values shall be kept
Returns:
The new Data object where bad quality values are not contained anymore

filterPQS

public static Data filterPQS(Data data,
                             LinearRegression l)
Filters data such that from each gene only one entry, the one with the lowest quality control value, is kept Commandline option pqs=min

Parameters:
data - Data object that shall be filtered
l - The linear regression object which will be used for the filtering
Returns:
The filtered Data object