makeWindowLookupTable {Repitools} | R Documentation

## Using the output of 'annotationLookup', create a tabular storage of the indices

### Description

To allow easy access to the probe-level data for either a gene, or an area of the promoter (over all genes), this routine takes the output of `annotationLookup` and organizes the indices into a table, one row for each gene and one column for each region of the promoter.

### Usage

      makeWindowLookupTable(indexes = NULL, offsets = NULL, starts = NULL, ends = NULL)

### Arguments

`indexes` | a list of indices, e.g. `indexes` element from `annotationLookup` output
`offsets` | a list of offsets, e.g. `offsets` element from `annotationLookup` output
`starts` | a vector of starts
`ends` | a vector of ends

### Details

The vectors `starts` and `ends` (which should be the same length) determine the number of columns in the output matrix.

### Value

A `matrix` with rows for each gene and columns for each bin of the promoter. `NA` signifies that there is no probe in the given distance from a TSS.

### Author(s)

Mark Robinson

### See Also

`annotationLookup`

### 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, 1000), end = c(3000, 2200), strand=c("+","-"))
    rownames(genes) <- paste("gene",1:2,sep="")

    # Call annotationLookup() and look at output
    aL <- annotationLookup(probeTab, genes, 500, 500)
    print(aL)

    # Store the results of annotationLookup() in a convenient tabular format
    lookupTab <- makeWindowLookupTable(aL$indexes, aL$offsets, starts=seq(-400,200,by=200), ends=seq(-200,400,by=200))
    print(lookupTab)

[Package Repitools version 1.30.0 Index]