matrix.snp_phased_ancestry: Creates a SNP phased, ancestry matrix.

In adelie: Group Lasso and Elastic Net Solver for Generalized Linear Models

Creates a SNP phased, ancestry matrix.

Description

Creates a SNP phased, ancestry matrix.

Usage

matrix.snp_phased_ancestry(io, n_threads = 1)

Arguments

io	IO handler.
n_threads	Number of threads.

Value

SNP phased, ancestry matrix.

Author(s)

James Yang, Trevor Hastie, and Balasubramanian Narasimhan
Maintainer: Trevor Hastie [e-mail]

Examples

n <- 123
s <- 423
A <- 8
filename <- paste(tempdir(), "snp_phased_ancestry_dummy.snpdat", sep="/")
handle <- io.snp_phased_ancestry(filename)
calldata <- matrix(
    as.integer(sample.int(
        2, n * s * 2,
        replace=TRUE,
        prob=c(0.7, 0.3)
    ) - 1),
    n, s * 2
)
ancestries <- matrix(
    as.integer(sample.int(
        A, n * s * 2,
        replace=TRUE,
        prob=rep_len(1/A, A)
    ) - 1),
    n, s * 2
)
handle$write(calldata, ancestries, A, 1)
out <- matrix.snp_phased_ancestry(handle)
file.remove(filename)

adelie documentation built on Sept. 11, 2024, 6:36 p.m.