annotationLookup: Forms a mapping between probes on a tiling array and windows...

In markrobinsonuzh/Repitools: Epigenomic tools

Forms a mapping between probes on a tiling array and windows surrounding the TSSs of genes.

Description

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

Usage

The data.frame,data.frame method:
annotationLookup(x, anno, ...)
The data.frame,GRanges method:
annotationLookup(x, anno, up, down, ...)

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.

up:

The number of bases upstream to look.

down:

The number of bases downstream to look.

verbose:

Whether to print progress to screen. Default: TRUE

...:

Parameters described above, that are not used in the function called, but are passed further into annotationBlocksLookup, which uses them in its processing.

Details

This function is a wrapper for the generic function annotationBlocksLookup which can handle annotations of varying sizes. annotationLookup is appropriate where you wish to map probes that are within a fixed distance of points of annotation e.g gene transcription start sites. Even if strand information is given for probes, it is ignored.

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.

It is an error for the gene annotation to have unstranded features.

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 genes' TSSs for each probe that mapped that that gene.

Author(s)

Aaron Statham, Mark Robinson

See Also

annotationBlocksLookup, makeWindowLookupTable

Examples

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

# Call annotationLookup() and look at output
annotationLookup(probes, genes, 500, 500)

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