Repitools (version 1.18.0)

annotationBlocksLookup: Forms a mapping between probe locations and chromosomal blocks (regions).

Description

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.

Usage

"annotationBlocksLookup"(x, anno, ...) "annotationBlocksLookup"(x, anno, verbose = TRUE)

Arguments

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.

Value

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.

Details

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.

See Also

annotationLookup which simplifies annotation lookups for constant sized regions

Examples

# 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)