n_missing: Count missing genotypes

In rqtl/qtl2geno: Treatment of Marker Genotypes for QTL Experiments

Description

Number (or proportion) of missing (or non-missing) genotypes by individual or marker

Usage

n_missing(cross, by = c("individual", "marker"), summary = c("count",
  "proportion"))

n_typed(cross, by = c("individual", "marker"), summary = c("count",
  "proportion"))

Arguments

cross	An object of class "cross2". For details, see the R/qtl2 developer guide.
by	Whether to summarize by individual or marker
summary	Whether to take count or proportion

Value

Vector of counts (or proportions) of missing (or non-missing) genotypes.

Functions

• n_missing: Count missing genotypes

• n_typed: Count genotypes

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
nmis_ind <- n_missing(iron)
pmis_mar <- n_typed(iron, "mar", "proportion")
plot(nmis_ind, xlab="Individual", ylab="No. missing genotypes")
plot(pmis_mar, xlab="Markers", ylab="Prop. genotyped")

rqtl/qtl2geno documentation built on May 28, 2019, 2:36 a.m.