pick_marker_subset: Identify the largest subset of markers that are some distance...
In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description Usage Arguments Details Value References Examples

Identify the largest subset of markers for which no two adjacent markers are separated by less than some specified distance; if weights are provided, find the marker subset for which the sum of the weights is maximized.

1	pick_marker_subset(map, min_d = 1, weights = NULL)

`map`	Either a vector of marker positions, or a list of such vectors (one vector per chromosome)
`min_d`	Minimum distance between markers
`weights`	An object of the same shape as `map`: either a vector of the same length, or a list with the same length and whose components are the same lengths.

Let d[i] be the location of marker i, for i in 1, …, M. We use the dynamic programming algorithm of Broman and Weber (1999) to identify the subset of markers i[1], …, i[k] for which d(i[j+1]) - d(i[j]) <= min.distance and sum w(i[j]) is maximized.

If there are multiple optimal subsets, we pick one at random.

The selected subset of marker positions, either as a vector or a list of vectors, according to the nature of map.

Broman KW, Weber JL (1999) Method for constructing confidently ordered linkage maps. Genet Epidemiol 16:337–343.

# load qtl2geno package for data and genoprob calculation
library(qtl2geno)

# read data
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2geno"))

# grap genetic map
gmap <- grav2$gmap

# subset to markers that are >= 1 cM apart
gmap_sub <- pick_marker_subset(gmap, 1)