gaston (version 1.4.9)

select.inds: Subsetting from a bed.matrix

Description

Return subset of individuals satisfying a condition.

Usage

select.inds(x, condition)

Arguments

x

A bed.matrix

condition

Condition used to select individuals

Value

bed.matrix similar to x, containing the selected individuals only

Details

The conditions can involve global variables, and all variables defined in the data frame x@ped, that is

• famid, id, father, mother, sex, pheno
• If basic stats have been computed (see set.stats), N0, N1, N2, NAs, callrate, etc.

If some condition evaluate to NA (e.g. sex == 1 when sex is undefined for some individuals), a warning is issued and the corresponding individuals are removed.

See Also

select.snps, set.stats

Examples

# Load data
data(LCT)
x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)

# Select individuals with a call rate > 95% 
# and more than 5% of heterozygous genotypes
y <- select.inds(x, callrate > 0.95 & N1/(N0+N1+N2) > 0.05)
y