wwhm: Window width at half maximum
In csaw: ChIP-Seq Analysis with Windows

Description Usage Arguments Details Value Author(s) See Also Examples

Get the width of the window from the half-maximum of the coverage profile.

1	wwhm(profile, regions, ext=100, proportion=0.5, rlen=NULL)

`profile`	a numeric vector containing a coverage profile, as produced by `profileSites`
`regions`	the `GRanges` object with which the profile was constructed
`ext`	an integer scalar specifying the average fragment length for single-end data
`proportion`	a numeric scalar specifying the proportion of the maximum coverage at which to compute the window width
`rlen`	a numeric scalar or vector containing read lengths, if any `ext=NA`, i.e., fragments are unextended reads

This function computes the ideal window size, based on the width of the peak in the coverage profile at the specified proportion of the maximum. Obviously, the values of regions and ext should be the same as those used in profileSites (set ext to the median fragment length for paired-end data). The regions should contain windows of a constant size.

Some subtleties are involved in obtaining the window width. First, twice the average fragment length must be subtracted from the peak width, as the profile is constructed from (inferred) fragments. The size of the viewpoints in regions must also be subtracted, to account for the inflated peak width when spatial resolution is lost after aggregation across many windows.

An integer scalar is returned, specifying the ideal window width.

Aaron Lun

profileSites, getWidths

x <- dnorm(-200:200/100) # Mocking up a profile.
windows <- GRanges("chrA", IRanges(1, 50)) # Making up some windows.

wwhm(x, windows)
wwhm(x, windows, ext=50)
wwhm(x, windows, proportion=0.2)

# Need to set 'rlen' if ext=NA.
wwhm(x, windows, ext=NA, rlen=10)