makeWindowLookupTable: Using the output of 'annotationLookup', create a tabular...

In markrobinsonuzh/Repitools: Epigenomic tools

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)

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