Function for mapping genomic features to probes

Description

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

Usage

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

Arguments

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?

Value

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.

Note

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.

Author(s)

Joern Toedling

See Also

regionOverlap

Examples

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   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]

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