The PLINK Input Engine imports a set of PLINK (Purcell et al., 2007) files into a SAS data set containing the marker genotypes and traits, and a SAS data set containing annotation (marker map) information.
Two different types of input files are required to run the PLINK Input Engine. The first type of file required lists specific pedigree, phenotype, and SNP genotype information for individuals in the study. Input data can be distributed among one or more files. Multiple files must be formatted as PED files, and each file must contain the same individuals. The test.ped file is shown below. This file is a space-delimited data set, individuals are in rows, and data for those individuals are in columns.
The second file required by the PLINK Input Engine is a map file, which contains physical location and other annotation information for each of the markers. The test.map map data set is shown below.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
The output data sets generated by this process are listed in a Results window. Refer to the PLINK Input Engine output documentation for detailed descriptions.