genio (version 1.1.2)

genio: genio (GENetics I/O): A package for reading and writing genetics data

Description

This package fully supports reading and writing Plink BED/BIM/FAM and GCTA GRM files, as illustrated below. These functions make it easy to create dummy annotation tables to go with simulated genotype data too. Lastly, there is functionality to read and write Eigenstrat tables.

Author

Maintainer: Alejandro Ochoa (ORCID)

See Also

Useful links:

• https://github.com/OchoaLab/genio

• Report bugs at https://github.com/OchoaLab/genio/issues

Examples

# read existing BED/BIM/FAM files

# first get path to BED file
file <- system.file( "extdata", 'sample.bed', package = "genio", mustWork = TRUE )

# read genotypes and annotation tables
plink_data <- read_plink( file )
# genotypes
X <- plink_data$X
# locus annotations
bim <- plink_data$bim
# individual annotations
fam <- plink_data$fam

# the same works without .bed extension
file <- sub( '\\.bed$', '', file ) # remove extension
plink_data <- read_plink( file )

# write data into new BED/BIM/FAM files
file_out <- tempfile( 'delete-me-example' )
write_plink( file_out, X, bim, fam )

# delete example files when done
delete_files_plink( file_out )

# read sample GRM files
file <- system.file( "extdata", 'sample.grm.bin', package = "genio", mustWork = TRUE )
file <- sub( '\\.grm\\.bin$', '', file ) # remove extension from this path on purpose
obj <- read_grm( file )
# the kinship matrix
kinship <- obj$kinship
# the pair sample sizes matrix
M <- obj$M
# the fam and ID tibble
fam <- obj$fam

# write data into new GRM files
write_grm( file_out, kinship, M = M, fam = fam )

# delete example files when done
delete_files_grm( file_out )

# other functions not shown here allow reading and writing individual files,
# creating dummy tables to go with simulated genotypes,
# requiring the existence of these files,
# and reading and writing of Eigenstrat tables too.