prune.distance: Prune markers by physical position

In tobyjohnson/gtx: Genetics ToolboX

Description

Selects subset of markers so that all excluded markers are within threshold physical distance of included markers.

Usage

prune.distance(chr, pos, pval, win.size = 500000)

Arguments

chr	A vector of chromosome locations
pos	A vector of position (on chromosome) locations
pval	A vector of p-values to order by
win.size	Threshold distance

Details

The pruning is done so that prune is TRUE only if there is no smaller P-value within win.size distance.

Value

A logical vector.

Author(s)

Toby Johnson [e-mail]

Examples

tophits <- data.frame(chr = floor(runif(1000, 1, 22.99)),
                      pos = floor(runif(1000, 1, 1000000.99)),
                      pval = runif(1000))
tophits <- tophits[order(tophits$pval), ]
tophits <- within(tophits, prune <- prune.distance(chr, pos, pval))
head(tophits, 20)
with(tophits, table(chr[prune]))

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.