drop_nullmarkers: Drop markers with no genotype data

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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)

qtl2 documentation built on April 22, 2023, 1:10 a.m.