getBindLen: Estimate length of binding and support region
Description
The cross-correlation between forward and reverse strand read counts is used to estimate the distance between
peaks on both strands. This is then used to derive suitable values for the length of binding and support regions.
Usage
getBindLen(data, bind, support, summary = median, verbose = FALSE, plot = TRUE, ...)
Arguments
data
An object of class ReadCounts.
bind
Either known length of binding region or minimum and maximum of binding region length to consider.
support
Either known length of support region or minimum and maximum of support region length to consider.
summary
Function to use to summarise cross-correlation across chromosomes.
verbose
Logical indicating whether progress messages should be printed.
plot
Logical indicating whether cross-correlation should be plotted.
Value
A numeric vector giving the estimated lengths of binding and support regions.
Details
This assumes that the first peak in cross-correlation corresponds to the length of the binding site.
Note that this is not accurate. The peak is closer to bind + 2*m where m is the median of the
read distribution in the support region ('read distribution in the support region' means the read
density as a function of distance to binding site start/end). Consequently this method will
overestimate the length of the binding site. If either bind or support are of length 1
this is assumed to be the known value and a more accurate estimate for the remaining parameter is used.