Collaboration diagram for umms.esat.ESATDistanceCalculator:

Public Member Functions
	ESATDistanceCalculator (String[] args) throws IOException, ParseException

Static Public Member Functions
static void	writeNormalizedMatrix (String fileName, MatrixWithHeaders resultMatrix) throws IOException

static Map< String, Double >	calculateNormalizationFactors (MatrixWithHeaders mat)

static List< Double >	array2List (double[] array)

static Gene	getSubAnnotationFromEnd (Gene annotation, int length, int distanceFromTranscriptEnd)

static Gene	getSubAnnotationFromStart (Gene annotation, int length, int distanceFromTranscriptStart)

static BEDFileParser	reconstructGeneEnds (BEDFileParser completeReconstruction, BEDFileParser annotations, String annotationFile) throws IOException

static void	main (String[] args) throws ParseException, IOException

Static Public Attributes
static String	whitespaceDelimiter = "\\s++"

Detailed Description

Author: skadri

Constructor & Destructor Documentation

umms.esat.ESATDistanceCalculator.ESATDistanceCalculator ( String[] args ) throws IOException, ParseException

If user wants to reconstruct gene ends.

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Member Function Documentation

static List<Double> umms.esat.ESATDistanceCalculator.array2List ( double[] array )

static

This function converts an array of double to List of type Double

Parameters

double[]

Returns

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static Map<String,Double> umms.esat.ESATDistanceCalculator.calculateNormalizationFactors ( MatrixWithHeaders mat )

static

Calculates the scaling factor for each column of the specified matrix, using the normalization method used by DESeq.

Parameters

mat

Returns

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static Gene umms.esat.ESATDistanceCalculator.getSubAnnotationFromEnd	(	Gene	annotation,
		int	length,
		int	distanceFromTranscriptEnd
	)

static

Returns the subannotation of length "length" at a distance "distanceFromTranscriptEnd" from the 3' end of the gene

Parameters

annotation
length
distanceFromTranscriptEnd

Returns

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static Gene umms.esat.ESATDistanceCalculator.getSubAnnotationFromStart	(	Gene	annotation,
		int	length,
		int	distanceFromTranscriptStart
	)

static

Returns the subannotation of length "length" at a distance "distanceFromTranscriptStart" from the 5' end of the gene

Parameters

annotation
length
distanceFromTranscriptEnd

Returns

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static void umms.esat.ESATDistanceCalculator.main ( String[] args ) throws ParseException, IOException

static

Parameters

args

Exceptions

IOException
ParseException

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static BEDFileParser umms.esat.ESATDistanceCalculator.reconstructGeneEnds	(	BEDFileParser	completeReconstruction,
		BEDFileParser	annotations,
		String	annotationFile
	)		throws IOException

static

Returns the reconstructed annotation set based on the reconstruction provided

Parameters

completeReconstruction
annotations
annotationFile

Returns

Exceptions

IOException

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static void umms.esat.ESATDistanceCalculator.writeNormalizedMatrix	(	String	fileName,
		MatrixWithHeaders	resultMatrix
	)		throws IOException

static

This function takes an input count matrix and returns a normalized matrix, where a scaling factor is calculated for each sample, and all genes for that sample are scaled by this factor.

Parameters