findProbePositions {GeneRegionScan} | R Documentation |
Function that will the location of probes in a gene based on their sequence.
findProbePositions(object, gene, probeData=NULL,interval=NULL,directions="all",verbose=TRUE)
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") |
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
A vector of positions of each probe in the object ProbeLevelSet, with names being probe ids
Lasse Folkersen
geneRegionScan
, plotOnGene
, plotCoexpression
data(exampleProbeLevelSet) findProbePositions(exampleProbeLevelSet, mrna)