findProbePositions {GeneRegionScan} | R Documentation

## 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")

### 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)

[Package GeneRegionScan version 1.50.0 Index]