Provides access to gene expression data from GNF. More...

Inheritance diagram for cls.HSGeneAtlasHandling.CHSGeneAtlasHandling:

Collaboration diagram for cls.HSGeneAtlasHandling.CHSGeneAtlasHandling:

Public Member Functions
def	__init__ (s, paths)
	Constructor. More...

def	SetProbeSetFilter (s, level=None)
	Set level of probes to include. More...

def	SetExpressionThreshold (s, th=None)
	Set threshold for expression. More...

def	SetExpressionFilter (s, direction="both")
	Specify how to use the threshold. More...

def	SetTissues (s, tissues=GA_TOI)
	Select tissues for output. More...

def	QueryExpressionHeader (s)
	Get the header names for the current settings. More...

def	QueryExpression (s, ncbiID, emptyCell=CELL_NO_DATA)
	Get the expression values for an Entrez gene. More...

Static Public Attributes
	paths = CPaths();

	ga = CHSGeneAtlasHandling(paths);

Detailed Description

Provides access to gene expression data from GNF.

In a 2004 publication entitled 'A gene atlas of the mouse and human
protein-encoding transcriptomes', Su et al describe an mRNA expression
experiment, where almost all known human genes were screened for
expression levels using Affymetrix microchip arrays. This class allows
access to these data.

Constructor & Destructor Documentation

◆ init()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.__init__	(	s,
		paths
	)

Constructor.

    @param  paths @c CPaths object for versioned file name retrieval.

Member Function Documentation

◆ QueryExpression()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.QueryExpression	(	s,
		ncbiID,
		emptyCell = `CELL_NO_DATA`
	)

Get the expression values for an Entrez gene.

    @param ncbiID  NCBI Entrez Gene ID.
    @param emptyCell  Empty cell identifier for genes that do not have any
     registered expression level, or for tissues that did not pass the
     threshold filter.
    @return  @c List of [@c probe_set_id, @c val1, @c val2, ...].

◆ QueryExpressionHeader()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.QueryExpressionHeader ( s )

Get the header names for the current settings.

Returns: List of Strings.

◆ SetExpressionFilter()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.SetExpressionFilter	(	s,
		direction = `"both"`
	)

Specify how to use the threshold.

    This filter is effective only if the threshold has been set to a
    numerical value via @ref SetExpressionThreshold.
    @param direction  One of (@c over-expressed, @c under-expressed, @c
     both). For @c over-expressed, genes will be reported if their
     expression level is greater than the threshold. Conversely, for @c
     under-expressed, only genes will be reported with levels below the
     negative threshold. If @c both is set, absolute values of expression
     levels higher than the threshold are output.
    @return  @c True, if the filter was set, @c False if the @c direction
     keyword was not recognized.

◆ SetExpressionThreshold()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.SetExpressionThreshold	(	s,
		th = `None`
	)

Set threshold for expression.

    Since genes are often targeted by multiple probe sets, it can be
    advantageous to remove genes which are expressed at moderate
    levels. Setting a threshold here will remove all genes with expression
    between @c -th and/or @c +th, see also @ref SetExpressionFilter. The
    threshold can be @c None to indicate that everything should be
    reported.
    @param th  Expression level threshold or @c None.
    @return @c True, if threshold was valid and accepted, @c False if
     rejected.

◆ SetProbeSetFilter()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.SetProbeSetFilter	(	s,
		level = `None`
	)

Set level of probes to include.

    The Gene Atlas stores a range of reliable and less reliable probe
    sets. Choice can be made here for which probe sets to include.
    @param level  @c at, single transcript target; @c s_at, multiple
     transcripts shared by a common sequence; @c x_at, targets ambiguously
     multiple sequences. @c None, ignore this filter, use all data.
    @return @c True, if filter was accepted; @c False if rejected.

◆ SetTissues()

def cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.SetTissues	(	s,
		tissues = `GA_TOI`
	)

Select tissues for output.

    Only the tissues selected here will be reported henceforth.
    @param tissues  @c List of tissue names. A list of allowed tissue
     names is given by @c GA_TOI.
    @return @c True, if the tissue have been set. @c False, if something
     went wrong, eg. a tissue name was incorrect.

Member Data Documentation

◆ ga

cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.ga = CHSGeneAtlasHandling(paths);

static

◆ paths

cls.HSGeneAtlasHandling.CHSGeneAtlasHandling.paths = CPaths();