qtl2 (version 0.24)

drop_nullmarkers: 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.

Value

The input cross with the uninformative markers removed.

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.

See Also

drop_markers(), pull_markers()

Examples

# NOT RUN {
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)
# }