R: Subsetting from a 'bed.matrix'

select.snps {gaston}

R Documentation

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

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

[Package gaston version 1.6 Index]

Subsetting from a bed.matrix