insert_pseudomarkers: Insert pseudomarkers into a marker map

In simecek/qtl2: Tools for analyzing high-dimensional QTL experiments

Description

Insert pseudomarkers into a map of genetic markers, for a single chromosome.

Usage

insert_pseudomarkers(map, step = 0, off_end = 0, stepwidth = c("fixed",
  "max"), pseudomarker_map, tol = 0.01)

Arguments

map	A list of numeric vectors; each vector gives marker positions for a single chromosome.
step	Distance between pseudomarkers and markers; if step=0 no pseudomarkers are inserted.
off_end	Distance beyond terminal markers in which to insert pseudomarkers.
stepwidth	Indicates whether to use a fixed grid (stepwidth="fixed") or to use the maximal distance between pseudomarkers to ensure that no two adjacent markers/pseudomarkers are more than step apart.
pseudomarker_map	A map of pseudomarker locations; if provided the step, off_end, and stepwidth arguments are ignored.
tol	Tolerance for determining whether a pseudomarker would duplicate a marker position.

Details

If stepwidth="fixed", a grid of pseudomarkers is added to the marker map.

If stepwidth="max", a minimal set of pseudomarkers are added, so that the maximum distance between adjacent markers or pseudomarkers is at least step. If two adjacent markers are separated by less than step, no pseudomarkers will be added to the interval. If they are more then step apart, a set of equally-spaced pseudomarkers will be added.

If pseudomarker_map is provided, then the step, off_end, and stepwidth arguments are ignored, and the input pseudomarker_map is taken to be a grid of pseudomarkers.

Value

A vector of positions of pseudomarkers and markers: the input map vector with pseudomarker positions added. An attribute "index" is an integer vector that indicates which positions are pseudomarkers (value -1) and which are markers (positive values, indicating the marker indices, (starting at 0).) If stepwidth=fixed (or if pseudomarker_map is provided), a further attribute ("grid") is a logical vector that indicates which positions correspond to the fixed grid.

Examples

library(qtl)
data(hyper)
map <- pull.map(hyper)
map_w_pmar <- insert_pseudomarkers(map, step=1)

simecek/qtl2 documentation built on May 29, 2019, 10:01 p.m.