A PCL set manages a collection of CPCL objects and aligns their gene indices. More...
#include <pclset.h>
Public Member Functions | |
| bool | Open (const std::vector< std::string > &vecstrFiles, size_t iSkip=2, CPCL::ENormalize eNormalize=CPCL::ENormalizeNone) |
| Create a new PCL set by opening and aligning the given PCL filenames. | |
| size_t | GetGenes () const |
| Return the number of genes in the PCL set. | |
| size_t | GetPCLs () const |
| Return the number of PCLs in the set. | |
| float | Get (size_t iPCL, size_t iGene, size_t iExperiment) const |
| Returns the value at the requested PCL position. | |
| const float * | Get (size_t iPCL, size_t iGene) const |
| Return a single gene's row from the given PCL. | |
| size_t | GetGene (const std::string &strGene) const |
| Return the index of the given gene name, or -1 if it is not included in the PCL set. | |
| const std::string & | GetGene (size_t iGene) const |
| Returns the gene name at the given index. | |
| const std::vector< std::string > & | GetGeneNames () const |
| Returns the vector of gene names associated with this PCL set. | |
| const CPCL & | Get (size_t iPCL) const |
| Return the PCL at the given index. | |
Detailed Description
A PCL set manages a collection of CPCL objects and aligns their gene indices.
A PCL set is a set of PCLs whose gene indices have been aligned; that is, the same gene will appear at any index in all contained PCLs. Genes not actually present in individual PCLs will be given missing values for data and empty strings for feature values.
- See also:
- IDataset
Member Function Documentation
| float Sleipnir::CPCLSet::Get | ( | size_t | iPCL, |
| size_t | iGene, | ||
| size_t | iExperiment | ||
| ) | const [inline] |
Returns the value at the requested PCL position.
- Parameters:
-
iPCL PCL index. iGene Gene row. iExperiment Experiment column.
- Returns:
- Value at the requested PCL position.
- Remarks:
- For efficiency, no bounds checking is performed. The given values must be smaller than GetPCLs, GetGenes, and that PCL's GetExperiments. Note that the gene index is within the PCL set, not the individual PCL; the experiment index is within the individual PCL.
Definition at line 93 of file pclset.h.
References Sleipnir::CFullMatrix< tType >::Get(), Sleipnir::CPCL::Get(), and Sleipnir::CMeta::GetNaN().
| const float* Sleipnir::CPCLSet::Get | ( | size_t | iPCL, |
| size_t | iGene | ||
| ) | const [inline] |
Return a single gene's row from the given PCL.
- Parameters:
-
iPCL PCL index. iGene Gene row.
- Returns:
- Requested PCL row.
- Remarks:
- For efficiency, no bounds checking is performed. The given values must be smaller than GetPCLs and GetGenes. Note that the gene index is within the PCL set, not the individual PCL.
Definition at line 118 of file pclset.h.
References Sleipnir::CFullMatrix< tType >::Get(), and Sleipnir::CPCL::Get().
| const CPCL& Sleipnir::CPCLSet::Get | ( | size_t | iPCL | ) | const [inline] |
Return the PCL at the given index.
- Parameters:
-
iPCL Index of PCL to retrieve from the set.
- Returns:
- PCL at the requested index.
- Remarks:
- For efficiency, no bounds checking is performed. The given index must be smaller than GetPCLs. Note that no gene alignment is done within the original PCL object.
| size_t Sleipnir::CPCLSet::GetGene | ( | const std::string & | strGene | ) | const [inline] |
Return the index of the given gene name, or -1 if it is not included in the PCL set.
- Parameters:
-
strGene Gene name to retrieve.
- Returns:
- Index of the requested gene name, or -1 if it is not in the PCL set.
- See also:
- GetGeneNames
| const std::string& Sleipnir::CPCLSet::GetGene | ( | size_t | iGene | ) | const [inline] |
| const std::vector<std::string>& Sleipnir::CPCLSet::GetGeneNames | ( | ) | const [inline] |
| size_t Sleipnir::CPCLSet::GetGenes | ( | ) | const [inline] |
| size_t Sleipnir::CPCLSet::GetPCLs | ( | ) | const [inline] |
| bool Sleipnir::CPCLSet::Open | ( | const std::vector< std::string > & | vecstrFiles, |
| size_t | iSkip = 2, |
||
| CPCL::ENormalize | eNormalize = CPCL::ENormalizeNone |
||
| ) |
Create a new PCL set by opening and aligning the given PCL filenames.
- Parameters:
-
vecstrFiles Vector of PCL filenames to be opened. iSkip Number of feature columns to skip between the gene IDs and experimental data columns in each file. eNormalize Way in which each PCL should be normalized.
- Returns:
- True if the PCL set was opened successfully.
- Remarks:
- The same number of skip columns must be used for each PCL in the set.
Definition at line 61 of file pclset.cpp.
References Sleipnir::CPCL::GetGene(), Sleipnir::CPCL::GetGenes(), Sleipnir::CFullMatrix< tType >::Initialize(), Sleipnir::CPCL::Normalize(), and Sleipnir::CFullMatrix< tType >::Set().
The documentation for this class was generated from the following files:
- src/pclset.h
- src/pclset.cpp
