insert_pseudomarkers: Insert pseudomarkers into a marker map

Description

Insert pseudomarkers into a map of genetic markers

Usage

insert_pseudomarkers(
  map,
  step = 0,
  off_end = 0,
  stepwidth = c("fixed", "max"),
  pseudomarker_map = NULL,
  tol = 0.01,
  cores = 1
)

Value

A list like the input map with pseudomarkers inserted. Will also have an attribute "is_x_chr", taken from the input map.

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.
cores: Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

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 the set of pseudomarker positions.

Examples

Run this code

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)