Package: genio 1.1.4.9000

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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genio.pdf |genio.html✨
genio/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

37 exports 17 stars 2.37 score 31 dependencies 3 dependents 145 scripts 701 downloads

Last updated 25 days agofrom:c5fa573ea5. Checks:OK: 2 ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 24 2024
R-4.5-win-x86_64ERRORAug 24 2024
R-4.5-linux-x86_64OKAug 24 2024
R-4.4-win-x86_64ERRORAug 24 2024
R-4.4-mac-x86_64ERRORAug 24 2024
R-4.4-mac-aarch64ERRORAug 24 2024
R-4.3-win-x86_64ERRORAug 24 2024
R-4.3-mac-x86_64ERRORAug 24 2024
R-4.3-mac-aarch64ERRORAug 24 2024

Exports:count_linesdelete_files_grmdelete_files_phendelete_files_plinkgeno_to_charhet_reencode_bedind_to_fammake_bimmake_famread_bedread_bimread_eigenvecread_famread_grmread_indread_matrixread_phenread_plinkread_snprequire_files_grmrequire_files_phenrequire_files_plinksex_to_charsex_to_intsim_and_write_plinksymlinktidy_kinshipwrite_bedwrite_bimwrite_eigenvecwrite_famwrite_grmwrite_indwrite_matrixwrite_phenwrite_plinkwrite_snp

Dependencies:bitbit64clicliprcpp11crayondplyrfansigenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR.methodsS3R.ooR.utilsR6Rcppreadrrlangtibbletidyselecttzdbutf8vctrsvroomwithr

Read and write BED files with genio

Alejandro Ochoa

Rendered fromgenio.Rmdusingknitr::rmarkdownon Aug 24 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Count the number of lines of a filecount_lines
Delete all GCTA binary GRM filesdelete_files_grm
Delete PHEN filesdelete_files_phen
Delete all Plink binary filesdelete_files_plink
genio (GENetics I/O): A package for reading and writing genetics datagenio-package genio
Convert a genotype matrix from numeric to character codesgeno_to_char
Reencode a Plink BED file to (twice) heterozygote indicatorshet_reencode_bed
Convert an Eigenstrat IND tibble into a Plink FAM tibbleind_to_fam
Create a Plink BIM tibblemake_bim
Create a Plink FAM tibblemake_fam
Read a genotype matrix in Plink BED formatread_bed
Read Plink *.bim filesread_bim
Read Plink eigenvec fileread_eigenvec
Read Plink *.fam filesread_fam
Read GCTA GRM and related plink2 binary filesread_grm
Read Eigenstrat *.ind filesread_ind
Read a numerical matrix file into an R matrixread_matrix
Read *.phen filesread_phen
Read genotype and sample data in a Plink BED/BIM/FAM file set.read_plink
Read Eigenstrat *.snp filesread_snp
Require that GCTA binary GRM files are presentrequire_files_grm
Require that PHEN file is presentrequire_files_phen
Require that Plink binary files are presentrequire_files_plink
Convert integer sex codes to character codessex_to_char
Convert character sex codes to integer codessex_to_int
Simulate and write genotypes to plink format on the flysim_and_write_plink
Create a symbolic link to a file, adjusting paths automatically if neededsymlink
Create a tidy version of a kinship matrixtidy_kinship
Write a genotype matrix into Plink BED formatwrite_bed
Write Plink *.bim fileswrite_bim
Write eigenvectors table into a Plink-format filewrite_eigenvec
Write Plink *.fam fileswrite_fam
Write GCTA GRM and related plink2 binary fileswrite_grm
Write Eigenstrat *.ind fileswrite_ind
Write a matrix to a file without row or column nameswrite_matrix
Write *.phen fileswrite_phen
Write genotype and sample data into a Plink BED/BIM/FAM file set.write_plink
Write Eigenstrat *.snp fileswrite_snp