'PLINK' (and 'GCTA') File Helpers
travers variants in a PLINK1 BED fileset
Read BED file
Read BIM file
Read Binary Symmetric Matrix (BSM)
Read FAM file
Read Genetic Related Matrix (GRM) of GCTA
Read PLINK Binary IBS matrix
read individual ID
Read PLINK Binary REL matrix
Read Variant Count Matrix (VCM) accompanying a GCTA GRM
read variant ID
Save BED file
Save Symmetric Matrix to Binary
Save symmetic matrix to GCTA GRM format.
Test BED Reader
Test Genetic Relatedness Matrix Reader
Reads/write binary genotype file compatible with 'PLINK' <https://www.cog-genomics.org/plink/1.9/input#bed> 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' <https://www.cog-genomics.org/plink/1.9/distance#make_rel> or 'GCTA' <https://cnsgenomics.com/software/gcta/#MakingaGRM> into/from a R square matrix. It is best used for bringing data produced by 'PLINK' and 'GCTA' into R workflow.