kin2gds: Store kinship matrix in GDS

In smgogarten/GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Store kinship matrix in GDS

Description

kin2gds and mat2gds write kinship matrices to GDS files.

Usage

kin2gds(ibdobj, gdsfile)
mat2gds(mat, gdsfile)

Arguments

ibdobj	A list with elements sample.id and kinship, such as the output of snpgdsIBDKING.
mat	A matrix with sample identifiers in colnames.
gdsfile	A character string with the name of the GDS file to create.

Details

When using pcair or pcairPartition with large sample sizes, it can be more memory efficient to read data from GDS files. kin2gds and mat2gds store kinship matrices in GDS files for use with these functions.

Author(s)

Stephanie M. Gogarten

See Also

kingToMatrix, snpgdsIBDKING

Examples

library(gdsfmt)

# KING results from the command-line program
file.kin0 <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS")
file.kin <- system.file("extdata", "MXL_ASW.kin", package="GENESIS")
KINGmat <- kingToMatrix(c(file.kin0, file.kin), estimator="Kinship")
gdsfile <- tempfile()
mat2gds(KINGmat, gdsfile)
gds <- openfn.gds(gdsfile)
gds
closefn.gds(gds)

# KING results from SNPRelate
library(SNPRelate)
geno <- snpgdsOpen(snpgdsExampleFileName())
king <- snpgdsIBDKING(geno)
closefn.gds(geno)
kin2gds(king, gdsfile)
gds <- openfn.gds(gdsfile)
gds
closefn.gds(gds)

smgogarten/GENESIS documentation built on Nov. 10, 2024, 8:49 p.m.