Package ubic.gemma.core.visualization.cellbrowser

Class CellBrowserTabularMatrixReader

java.lang.Object

ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader

public class CellBrowserTabularMatrixReader
extends Object

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
CellBrowserTabularMatrixReader()

Method Summary

Modifier and Type	Method	Description
SingleCellExpressionDataDoubleMatrix	readMatrix(Reader reader, QuantitationType quantitationType, Map<String,CompositeSequence> designElementsMap, Map<String,BioAssay> cellIdToBioAssayMap)	Read a single-cell data matrix from a Cell Browser-compatible format.
void	setIgnoreUnmatchedCellIds(boolean ignoreUnmatchedCellIds)	Ignore cell identifiers in the header for which no assay can be found instead of throwing an exception.
void	setIgnoreUnmatchedGenes(boolean ignoreUnmatchedGenes)	Ignore gene identifiers in the "gene" column for which no design element can be found instead of throwing an exception.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CellBrowserTabularMatrixReader

public CellBrowserTabularMatrixReader()

Method Details

readMatrix

public SingleCellExpressionDataDoubleMatrix readMatrix(Reader reader,
 QuantitationType quantitationType,
 Map<String,CompositeSequence> designElementsMap,
 Map<String,BioAssay> cellIdToBioAssayMap)
                                                throws IOException

Read a single-cell data matrix from a Cell Browser-compatible format.

Parameters:

reader - reader to read the matrix from

quantitationType - quantitation type to use for the resulting matrix. It affects how the values are parsed.

designElementsMap - a mapping of identifiers in the "gene" column to design elements.

Throws:

IOException

setIgnoreUnmatchedCellIds

public void setIgnoreUnmatchedCellIds(boolean ignoreUnmatchedCellIds)

Ignore cell identifiers in the header for which no assay can be found instead of throwing an exception.

setIgnoreUnmatchedGenes

public void setIgnoreUnmatchedGenes(boolean ignoreUnmatchedGenes)

Ignore gene identifiers in the "gene" column for which no design element can be found instead of throwing an exception.