Sleipnir::CSeekPlatform Class Reference

Representation of a microarray platform that is used by Seek. More...

#include <seekplatform.h>

Public Member Functions
	CSeekPlatform ()
	Constructor.
	~CSeekPlatform ()
	Destructor.
void	InitializePlatform (const utype &, const string &)
	Initialize the platform.
void	SetPlatformAvg (const utype &, const float &)
	Set the platform correlation average for a particular gene.
void	SetPlatformStdev (const utype &, const float &)
	Set the platform standard deviation of correlation for a given gene.
float	GetPlatformAvg (const utype &) const
	Get the platform-wide correlation average for a given gene.
float	GetPlatformStdev (const utype &) const
	Get the platform-wide standard deviation of correlation for a given gene.
void	ResetPlatform ()
	Reset.
void	Copy (const CSeekPlatform &)

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Detailed Description

Representation of a microarray platform that is used by Seek.

Contains the gene correlation average and standard deviation for a given platform

For each gene g in each dataset d, we calculate the average correlation of g to all the genes. Then average it across all the datasets in the platform. The result is the platform's gene-correlation average, or PlatformAvg for short.

The standard deviation or PlatformStdev measures the spread of correlation across all datasets of the given platform.

The purpose of the platform's average and standard deviation are to reduce potential biases that might be caused by platform specific correlation distributions.

Remarks:

The word correlation refers to z-score transformed, standardized Pearson correlation.

Definition at line 47 of file seekplatform.h.

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Member Function Documentation

void Sleipnir::CSeekPlatform::Copy

(

const CSeekPlatform &

pl

)

Create a copy from a given platform

Parameters:

pl	The given platform

Definition at line 39 of file seekplatform.cpp.

float Sleipnir::CSeekPlatform::GetPlatformAvg

(

const utype &

i

)

const

Get the platform-wide correlation average for a given gene.

Parameters:

i	Gene index

Returns:

The platform-wide average

Definition at line 66 of file seekplatform.cpp.

Referenced by Sleipnir::CSeekDataset::InitializeDataMatrix().

float Sleipnir::CSeekPlatform::GetPlatformStdev

(

const utype &

i

)

const

Get the platform-wide standard deviation of correlation for a given gene.

Parameters:

i	Gene index

Returns:

The platform-wide standard deviation

Definition at line 70 of file seekplatform.cpp.

Referenced by Sleipnir::CSeekDataset::InitializeDataMatrix().

void Sleipnir::CSeekPlatform::InitializePlatform	(	const utype &	numGenes,
		const string &	strPlatformName
	)

Initialize the platform.

Parameters:

numGenes	The number of genes covered by the platform
strPlatformName	Assign a name to the platform

Definition at line 50 of file seekplatform.cpp.

References Sleipnir::CSeekTools::InitVector().

void Sleipnir::CSeekPlatform::SetPlatformAvg	(	const utype &	i,
		const float &	val
	)

Set the platform correlation average for a particular gene.

Parameters:

i	Gene index
val	The average correlation for the gene

Definition at line 58 of file seekplatform.cpp.

void Sleipnir::CSeekPlatform::SetPlatformStdev	(	const utype &	i,
		const float &	val
	)

Set the platform standard deviation of correlation for a given gene.

Parameters:

i	Gene index
val	The standard deviation

Definition at line 62 of file seekplatform.cpp.

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The documentation for this class was generated from the following files:

• src/seekplatform.h
• src/seekplatform.cpp