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plinkFile (version 0.2.1)

'PLINK' (and 'GCTA') File Helpers

Description

Reads/write binary genotype file compatible with 'PLINK' into/from a R matrix; traverse genotype data one windows of variants at a time, like apply() or a for loop; reads/writes genotype relatedness/kinship matrices created by 'PLINK' or 'GCTA' into/from a R square matrix. It is best used for bringing data produced by 'PLINK' and 'GCTA' into R workflow.

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Version

Install

install.packages('plinkFile')

Monthly Downloads

230

Version

0.2.1

License

GPL (>= 2)

Maintainer

Xiaoran Tong

Last Published

November 24th, 2023

Functions in plinkFile (0.2.1)

readVCM

Read Variant Count Matrix (VCM) accompanying a GCTA GRM
saveBED

Save BED file
readVID

read variant ID
readBIM

Read BIM file
readIID

read individual ID
scanBED

travers variants in a PLINK1 BED fileset
readFAM

Read FAM file
readBED

Read BED file
readIBS

Read PLINK Binary IBS matrix
readGRM

Read Genetic Related Matrix (GRM) of GCTA
CHR

A dictionary to map chromosome names to integers.
DBT

A decoding byte table to map raw intergers to genotype dosages.
readBSM

Read Binary Symmetric Matrix (BSM)
saveBSM

Save Symmetric Matrix to Binary
readREL

Read PLINK Binary REL matrix
saveGRM

Save symmetic matrix to GCTA GRM format.
testReadBSM

Test Genetic Relatedness Matrix Reader
testReadBED

Test BED Reader