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plinkFile (version 0.1.0)

'PLINK' (and 'GCTA') File Helpers

Description

Provide function that reads binary genotype produced by 'PLINK' into a R matrix, or scan the genotype one variant at a time like apply(), it also provides functions that reads and writes genotype relatedness/kinship matrices created by 'PLINK' or 'GCTA' . Currently it does not support writing back into 'PLINK' binary, it is best used for bringing data produced by 'PLINK' and 'GCTA' into R environment.

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Version

Install

install.packages('plinkFile')

Monthly Downloads

230

Version

0.1.0

License

GPL (>= 2)

Maintainer

Xiaoran Tong

Last Published

April 5th, 2020

Functions in plinkFile (0.1.0)

testReadBED

Test BED Reader
testScanBED

Test BED Scanner
saveBSM

Save Symmetric Matrix to Binary
readVCM

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

Read Genetic Related Matrix (GRM) of GCTA
scanBED

Scan genotypes in PLINK BED(s)
saveGRM

Save symmetic matrix to GCTA GRM format.
testReadBSM

Test Genetic Relatedness Matrix Reader
readBIM

Read BIM file
readBSM

Read Binary Symmetric Matrix (BSM)
gid

Infer Sample ID from a symmetric matrix
readREL

Read PLINK Binary REL matrix
readBED

Read BED file
readFAM

Read FAM file
lc

Line Count
dbd

Decompress Byte Data
readIBS

Read PLINK Binary IBS matrix