makeWindowLookupTable {Repitools} | R Documentation |
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.
makeWindowLookupTable(indexes = NULL, offsets = NULL, starts = NULL, ends = NULL)
indexes |
a list of indices, e.g. |
offsets |
a list of offsets, e.g. |
starts |
a vector of starts |
ends |
a vector of ends |
The vectors starts
and ends
(which should be the same length) determine the number of columns in the output matrix.
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.
Mark Robinson
# 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)