annotationBlocksLookup: Forms a mapping between probe locations and chromosomal...
In Repitools: Epigenomic tools

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

Starting from a table of genome locations for probes, and a table of regions of interest, this procedure forms a list structure that contains the indices to map from one to the other.

  ## S4 method for signature 'data.frame,data.frame'
annotationBlocksLookup(x, anno, ...)
  ## S4 method for signature 'data.frame,GRanges'
annotationBlocksLookup(x, anno, verbose = TRUE)

`x`	probe genomic locations, a `data.frame` with required elements `chr`, `position`, and optionally `index`
`anno`	a `data.frame` with required elements `chr`, `start`, `end`, `strand` and optional element `name`. Also may be a `GRanges` with optional elementMetadata column `name`.
`verbose`	Whether to print progress to screen.
`...`	Represents the `verbose` parameter, when the `data.frame,data.frame` method is called.

Strandedness of probes is ignored, even if it is given.

If x has no index column, then the probes are given indices from 1 to the number of probes, in the order that they appear in the data.frame or GRanges object.

A list with elements

`indexes`	a list for each gene in `y`, giving a vector of indices to the probe data.
`offsets`	a list for each gebe in `y`, giving a vector (corresponding to `indexes`) of offsets relative to the start of the block.

Aaron Statham, Mark Robinson

annotationLookup which simplifies annotation lookups for constant sized regions

# create example set of probes and gene start sites
probeTab <- data.frame(position=seq(1000,3000,by=200), chr="chrX", strand="+")
genes <- data.frame(chr="chrX", start=c(2100,2200), end=c(2500, 2400), strand=c("+","-"))
rownames(genes) <- paste("gene",1:2,sep="")

# Call annotationLookup() and look at output
annotationBlocksLookup(probeTab, genes)