features2Probes: Function for mapping genomic features to probes
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Value Note Author(s) See Also Examples

This function creates a mapping between annotated genomic features and probes on the array whose matching genomic positions are stored in a probeAnno environment.

1	features2Probes(gff, probeAnno, upstream = 5000, checkUnique = TRUE, uniqueCodes = c(0), mem.limit=1e8, verbose = TRUE)

`gff`	`data.frame` holding genomic feature annotation
`probeAnno`	Object of class `environment` holding the genomic positions of probes in the ExpressionSet
`upstream`	up to how many bases upstream of annotated genomic features should probes be counted as related to that feature (see details)
`checkUnique`	logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
`uniqueCodes`	numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
`mem.limit`	integer value; what is the maximal allowed size of matrices during the computation; see `regionOverlap`
`verbose`	logical; detailed progress output to STDOUT?

The results is a list of length equal to the number of rows in the provided gff, the data.frame of genomic features. The names of the list are the names specified in the gff. Each element of the list is specified by the probes mapping into the genomic region from upstream bases upstream of the feature's start site to the feature's end site. The entries itself are either NULL, if no probe was mapped into this region, or a named numeric vector, with its values being the distances of the probes' middle positions to the feature's start site (which depends on the strand the feature is on) and its names being the identifiers of these probes.

This resulting mapping is not used excessively by other Ringo functions, so creating this mapping is optional at this time, but it may simplify subsequent gene/transcript-based analyses.

Here, the term feature describes a genomic entity such as a gene, transcript, non-coding RNA or a similar feature annotated to a genome. It does NOT refer to oligo-nucleotide or cDNA probes on the microarray.

Joern Toedling

regionOverlap

   ringoExampleDir <- system.file("exData",package="Ringo")
   load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
   trans2Probe <- features2Probes(exGFF, exProbeAnno)
   trans2Probe[exGFF$name[match("NUDT2", exGFF$symbol)]]
   exGFF[match(names(trans2Probe)[listLen(trans2Probe)>0],exGFF$name),]
   trans2Probe[listLen(trans2Probe)==1]