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== 3. Prepare PED file for phenotypes and covariates ==
== 3. Prepare PED file for phenotypes and covariates ==
EPACTS accepts the PED format supported by MERLIN or PLINK to represent the phenotypes and covariates. You may prepare either (1) a PED file without column headers + accompanying DAT file, or (2) a PED file with column headers.
EPACTS accepts the PED format supported by MERLIN or [http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml PLINK ]to represent the phenotypes and covariates. You may prepare either (1) a PED file without column headers + accompanying DAT file, or (2) a PED file with column headers. The standard PED format has 6 mandatory columns:
#Family ID
#Individual ID
#Paternal ID
#Maternal ID
#Sex (1=male; 2=female; other=unknown)
#Phenotype
Columns 7 and onwards are covariate information. For example
#AGE
#SEX
#PC1
#PC2
etc.
