marker.fill: Map Positions Between Markers

In bqtl: Bayesian QTL Mapping Toolkit

Map Positions Between Markers

Description

Given a set of markers, one wants to create a finer map at a given resolution. marker fill takes a a collection of marker distances and a desired resolution and finds positions that are intermediate and at that resolution.

Usage

marker.fill(map.frame, reso, return.nint = FALSE)

Arguments

map.frame	A map.frame.object.
reso	The desired interval between loci in the same metric as map.frame$cM
return.nint	Whether to output a vector of number of intervals to produce in each existing interlocus interval

Value

If return.nint is TRUE, a vector of integers is returned. It indicates how many intervals to place between this marker and the next to achive the desired minimum distance.

If return.nint is FALSE, a vector of distances is returned. The names attribute has suffixes added to indicate positions filled to the 'right' of existing markers. Thus if markers 'mark.01' and 'mark.02' are in succession at a distance of 3 and reso==1, then the value associated with 'mark.01' (which was 3) becomes 1, a value of 1 is associated with new loci called 'mark.01.1' and 'mark.01.2' in created with values of 1 each. The returned vector is ordered by chromosome, then marker or filled locus.

See Also

make.map.frame

Examples

data( little.map.frame  )
little.nint <- marker.fill( little.map.frame, reso=5, TRUE )
cbind(nint=little.nint,cM=little.map.frame$cM)[1:10,]
rm( little.map.frame, little.nint )

bqtl documentation built on Sept. 25, 2024, 1:08 a.m.