probs_to_grid: Subset genotype probability array to pseudomarkers on a grid
In rqtl/qtl2geno: Treatment of Marker Genotypes for QTL Experiments

Description Usage Arguments Details Value See Also Examples

Subset genotype probability array (from calc_genoprob() to a grid of pseudomarkers along each chromosome.

1	probs_to_grid(probs, grid)

`probs`	Genotype probabilities as output from `calc_genoprob()` with `stepwidth="fixed"`.
`grid`	List of logical vectors that indicate which positions are on the grid and should be retained.

This only works if calc_genoprob() was run with stepwidth="fixed", so that the genotype probabilities were calculated at a grid of markers/pseudomarkers. When this is the case, we omit all but the probabilities on this grid. Use calc_grid() to find the grid positions.

Same list as input, but subset to just include pseudomarkers along a grid. The map attribute is similarly subset.

calc_grid(), map_to_grid()

grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2geno"))
map_w_pmar <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map_w_pmar, error_prob=0.002)
sapply(probs, dim)
grid <- calc_grid(grav2$gmap, step=1)
probs_sub <- probs_to_grid(probs, grid)
sapply(probs_sub, dim)