select.snps: Subsetting from a 'bed.matrix'

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Subsetting from a bed.matrix

Description

Returns subset of SNPs satisfying a condition.

Usage

 select.snps(x, condition) 

Arguments

x	A bed.matrix
condition	Condition used to select SNPs

Details

The conditions can involve global variables and all variables defined in the data frame x@snps, in particular

• chr, id, dist, pos, A1, A2

• If basic stats have been computed (see set.stats), N0, N1, N2, NAs, callrate, maf, hz, etc.

• If Hardy-Weinberg Equilibrium test has been performed (see set.hwe), hwe.

If some condition evaluate to NA (e.g. maf > 0 when maf is undefined for some SNPs), a warning is issued and the corresponding SNPs are removed.

Value

A bed.matrix similar to x, containing the selected SNPs only

Author(s)

Hervé Perdry and Claire Dandine-Roulland

See Also

select.snps, set.stats, set.hwe

Examples

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

# Select SNPs with a maf > 5%
y <- select.snps(x, maf > 0.05)
y

gaston documentation built on Dec. 28, 2022, 1:30 a.m.