findProbePositions: Find positions of probes on a gene

In GeneRegionScan: GeneRegionScan

Description

Function that will the location of probes in a gene based on their sequence.

Usage

    findProbePositions(object, gene, probeData=NULL,interval=NULL,directions="all",verbose=TRUE)

Arguments

object	A ProbeLevelSet object or a regular ExpressionSet object (in which case a probeData argument is required). See getLocalProbeIntensities and related functions on how to create a ProbeLevelSet.
gene	A number of gene sequences as DNAstring, DNAStringsSets, or character-vectors with sequence.
probeData	Optional if a ProbeLevelSet is submitted as object argument. Otherwise, it must be a data frame with rownames corresponding to the featureNames of the ExpressionSet and a column named "sequence" with the probe sequences as character strings
interval	Optional vector of two integers of bp positions. If given, the plot will only include the sequence from gene in the given interval. The x-axis annotation is preserved from original, so this is useful for zooming on specific regions.
verbose	TRUE or FALSE
directions	A character vector of the matching-directions that should be scanned (which combinations of complementary and reverse). Defaults to "all" which is shorthand for all possible directions, but can take anything from: c("matchForwardSense", "matchForwardAntisense", "matchReverseSense", "matchReverseAntisense")

Details

This function is principally used by the plotOnGene to assign positions of each probe relative to the gene sequence of interest. In a recent version of GeneRegionScan it was separated as a discrete function because of its use in alternative plotting

Value

A vector of positions of each probe in the object ProbeLevelSet, with names being probe ids

Author(s)

Lasse Folkersen

See Also

geneRegionScan, plotOnGene, plotCoexpression

Examples

	data(exampleProbeLevelSet)
	
	findProbePositions(exampleProbeLevelSet, mrna)
	

GeneRegionScan documentation built on Nov. 8, 2020, 8:28 p.m.