readFAM {plinkFile} | R Documentation |
Read FAM file
Description
Read sample meta-data form the fam file of a PLINK1 BED fileset.
Usage
readFAM(fam)
Arguments
fam |
prefix or name of a PLINK file. |
Details
There are six columns in a bim file
fid: family ID;
iid: individual ID, default row name used by
[readBED]
;mom: maternal ID;
dad: paternal ID;
sex: individual sex.
phe: phenotype, not often used;
The PLINK1 bim file has no header line, this is changed in PLINK2.
The columns "sex" and "phe" are mostly the legency of early GWAS, nowerdays it is common to provide sex, among other covariates, and multiple phenotypes in a separate file.
Value
data frame of individuals, loaded from FAM.
Examples
pfx <- file.path(system.file("extdata", package="plinkFile"), "m20")
fam <- readFAM(pfx)
fam
[Package plinkFile version 0.2.1 Index]