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java.lang.Objecthalo.data.Filter
public class Filter
Provides methods for filtering the values contained in a Data object
Constructor Summary | |
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Filter()
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Method Summary | |
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static boolean |
checkForGenes(Data data)
Checks if the data object has the gene name attribute loaded and can be used for PQS filtering |
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> relevantColumns,
java.lang.String call,
int threshold)
Removes values that are defined as 'absent' in the attribute list Commandline option -f present='label1,label2,... |
static Data |
filterCorrectionBias(Data data,
java.util.HashMap<java.lang.String,java.lang.Double> corr)
Filters the data according to given values for bias correction in such a way that only those probeset ids are kept that have corresponding correction values |
static Data |
filterPQS(Data data,
Normalization l,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
filterPQS(Data data,
Normalization l,
double threshold,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
filterPQS(Data data,
Normalization l,
int replicate,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
transferAllValues(Data oldData,
Data newData)
Transfers all values that are not directly used in filtering from the old data object to the new data object |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Filter()
Method Detail |
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public static Data filter(Data data, double threshold)
data
- Data object which shall be filteredthreshold
- Cutoff-threshold
public static Data filterAbsent(Data data, java.util.ArrayList<java.lang.String> relevantColumns, java.lang.String call, int threshold)
data
- Data object that will be filteredrelevantColumns
- List of the labels of all columns that contain call informationcall
- The call according to which will be filtered, usually 'A' for absentthreshold
- Defines how often the $call has to be noted for one spotid for it to be filtered
public static Data filterPQS(Data data, Normalization l, double threshold, boolean histogram)
data
- Data object that shall be filteredl
- Linear Regression object which correction factors will be used for filteringthreshold
- A threshold which defines which values shall be kepthistogram
- TRUE if a histogram about the PQS values should be produced, FALSE otherwise
public static Data filterPQS(Data data, Normalization l, int replicate, boolean histogram)
data
- Data object that shall be filteredl
- The normalization object which will be used for the filteringreplicate
- The replicate for which the ratio calculation will be performedhistogram
- TRUE if a histogram about the PQS values should be produced, FALSE otherwise
public static Data filterPQS(Data data, Normalization l, boolean histogram)
data
- Data object that shall be filteredl
- The normalization object which will be used for the filteringhistogram
- TRUE if a histogram about the PQS values should be produced, FALSE otherwise
public static Data filterCorrectionBias(Data data, java.util.HashMap<java.lang.String,java.lang.Double> corr)
data
- The original data objectcorr
- The correction values, mapped from id -> value
public static Data transferAllValues(Data oldData, Data newData)
oldData
- The data object before filteringnewData
- The new data object, created while filtering
public static boolean checkForGenes(Data data)
data
- The data object
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