findProbePositions: Find positions of probes on a gene

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")

Value

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

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

Examples

Run this code

data(exampleProbeLevelSet)
	
	findProbePositions(exampleProbeLevelSet, mrna)

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