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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 [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:
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
#Family ID
#Individual ID
#Individual ID
#Paternal ID
#Paternal ID
#Maternal ID
#Maternal ID
#Sex (1=male; 2=female; other=unknown)
#Sex (1=male; 2=female; other=unknown)
#Phenotype
#Phenotype
Columns 7 and onwards are covariate information. For example
Columns 7 and onwards are additonal covariates and or phenotypes. For example
#QT
#AGE
#AGE
#PC1
#PC1
etc.
etc.
An example PED file with a header is as follows:
<pre>#FAM_ID IND_ID FAT_ID MOT_ID SEX DISEASE QT AGE
13281 NA12344 NA12347 NA12348 1 1 94.17 66.1
13281 NA12347 0 0 1 1 109.54 44.0
13281 NA12348 0 0 2 2 119.40 46.6
1328 NA06984 0 0 1 2 87.72 39.3
1328 NA06989 0 0 2 1 100.60 41.7
1328 NA12329 NA06984 NA06989 2 1 100.85 46.4
13291 NA06986 0 0 1 2 91.94 61.9
13291 NA06995 NA07435 NA07037 1 2 104.36 57.4
13291 NA06997 NA06986 NA07045 2 2 107.53 53.1
</pre>
Alternatively, you can prepare a PED file without a header, and include a corresponding DAT file describing the column headers
13281 NA12344 NA12347 NA12348 1 1 94.17 66.1<br>13281 NA12347 0 0 1 1 109.54 44.0<br>13281 NA12348 0 0 2 2 119.40 46.6<br>1328 NA06984 0 0 1 2 87.72 39.3<br>1328 NA06989 0 0 2 1 100.60 41.7<br>1328 NA12329 NA06984 NA06989 2 1 100.85 46.4<br>13291 NA06986 0 0 1 2 91.94 61.9<br>13291 NA06995 NA07435 NA07037 1 2 104.36 57.4<br>13291 NA06997 NA06986 NA07045 2 2 107.53 53.1<br><br>
