drop_nullmarkers {qtl2}

Drop markers with no genotype data

Description

Drop markers with no genotype data (or no informative genotypes)

Usage

drop_nullmarkers(cross, quiet = FALSE)

Arguments

cross

Object of class "cross2". For details, see the R/qtl2 developer guide.

quiet

If FALSE, print information about how many markers were dropped.

Details

We omit any markers that have completely missing data, or if founder genotypes are present (e.g., for Diversity Outbreds), the founder genotypes are missing or are all the same.

Value

The input cross with the uninformative markers removed.

See Also

drop_markers(), pull_markers()

Examples

grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
# make a couple of markers missing
grav2$geno[[2]][,c(3,25)] <- 0
grav2_rev <- drop_nullmarkers(grav2)