Package: genio 1.1.6.9000

Alejandro Ochoa

genio: Genetics Input/Output Functions

Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.

Authors:Alejandro Ochoa [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genio/json (API)

# Install 'genio' in R:

install.packages('genio', repos = c('https://ochoalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ochoalab/genio/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

7.93 score 18 stars 6 packages 447 scripts 1.2k downloads 37 exports 30 dependencies

Last updated from:b776208acc. Checks:6 OK, 7 ERROR. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	159
linux-devel-x86_64	OK	145
source / vignettes	OK	207
linux-release-arm64	OK	182
linux-release-x86_64	OK	155
macos-release-arm64	ERROR	101
macos-release-x86_64	ERROR	225
macos-oldrel-arm64	ERROR	122
macos-oldrel-x86_64	ERROR	256
windows-devel	ERROR	133
windows-release	ERROR	142
windows-oldrel	ERROR	117
wasm-release	OK	143

Exports:count_lines delete_files_grm delete_files_phen delete_files_plink geno_to_char het_reencode_bed ind_to_fam make_bim make_fam read_bed read_bim read_eigenvec read_fam read_grm read_ind read_matrix read_phen read_plink read_snp require_files_grm require_files_phen require_files_plink sex_to_char sex_to_int sim_and_write_plink symlink tidy_kinship write_bed write_bim write_eigenvec write_fam write_grm write_ind write_matrix write_phen write_plink write_snp

Dependencies:bit bit64 cli clipr cpp11 crayon dplyr generics glue hms lifecycle magrittr pillar pkgconfig prettyunits progress R.methodsS3 R.oo R.utils R6 Rcpp readr rlang tibble tidyselect tzdb utf8 vctrs vroom withr

Read and write BED files with genio

Rendered fromgenio.Rmdusingknitr::rmarkdown

Last update: 2021-07-26
Started: 2019-05-17

Help page	Topics
Count the number of lines of a file	count_lines
Delete all GCTA binary GRM files	delete_files_grm
Delete PHEN files	delete_files_phen
Delete all Plink binary files	delete_files_plink
genio (GENetics I/O): A package for reading and writing genetics data	genio-package genio
Convert a genotype matrix from numeric to character codes	geno_to_char
Reencode a Plink BED file to (twice) heterozygote indicators	het_reencode_bed
Convert an Eigenstrat IND tibble into a Plink FAM tibble	ind_to_fam
Create a Plink BIM tibble	make_bim
Create a Plink FAM tibble	make_fam
Read a genotype matrix in Plink BED format	read_bed
Read Plink *.bim files	read_bim
Read Plink eigenvec file	read_eigenvec
Read Plink *.fam files	read_fam
Read GCTA GRM and related plink2 binary files	read_grm
Read Eigenstrat *.ind files	read_ind
Read a numerical matrix file into an R matrix	read_matrix
Read *.phen files	read_phen
Read genotype and sample data in a Plink BED/BIM/FAM file set.	read_plink
Read Eigenstrat *.snp files	read_snp
Require that GCTA binary GRM files are present	require_files_grm
Require that PHEN file is present	require_files_phen
Require that Plink binary files are present	require_files_plink
Convert integer sex codes to character codes	sex_to_char
Convert character sex codes to integer codes	sex_to_int
Simulate and write genotypes to plink format on the fly	sim_and_write_plink
Create a symbolic link to a file, adjusting paths automatically if needed	symlink
Create a tidy version of a kinship matrix	tidy_kinship
Write a genotype matrix into Plink BED format	write_bed
Write Plink *.bim files	write_bim
Write eigenvectors table into a Plink-format file	write_eigenvec
Write Plink *.fam files	write_fam
Write GCTA GRM and related plink2 binary files	write_grm
Write Eigenstrat *.ind files	write_ind
Write a matrix to a file without row or column names	write_matrix
Write *.phen files	write_phen
Write genotype and sample data into a Plink BED/BIM/FAM file set.	write_plink
Write Eigenstrat *.snp files	write_snp

Package: genio 1.1.6.9000

genio: Genetics Input/Output Functions

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