annotationBlocksLookup: Forms a mapping between probe locations and chromosomal...

In markrobinsonuzh/Repitools: Epigenomic tools

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

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

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.

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.

Author(s)

Aaron Statham, Mark Robinson

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)

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.