.bed files must be
accompanied by .fam
and .bim files:
.fam files contain sample information, and .bim files contain variant
information. If the name of the .bed file is plink.bed then the
names of the .fam and .bim files have to be plink.fam and
plink.bim, respectively. The .fam and .bim files are used to extract
the number and names of samples and variants.
For very large .bed files, reading the .fam and .bim files can take a long
time. If n
and p
are provided, these files are not read and
dimnames
have to be provided manually.
Currently, only the variant-major mode of .bed files is supported.
PLINK2 "dropped" support for
the sample-major mode by automatically converting files in this format to
the variant-major mode. Therefore, it is recommended to run files in
sample-major mode through PLINK2 first.