HapMap Input Engine

Running this process using the genotypes_chr1_CEU_r23_nr.b36_fwd.txt file generates the Results window shown below. Refer to the HapMap Input Engine process description for more information.

The Results window contains the following elements:

Output Data

This process generates the following data sets:

•	Genotype Data Set: This wide data set lists genotype for each marker. Alternatively, for markers for which no genotype's probability meets the specified threshold, a missing value symbol ( . ) is listed.

This data set can be very large. To avoid the problems opening large data sets can cause, JMP Genomics provides you with a way to view a sample of the output genotype data set. This option is especially useful when a quick assessment of the data set to assure correct formatting is all that is needed before proceeding to additional analyses.

Click View Subset in the SAS Message window.

The dialog for the JMP Genomics Check Data Contents process automatically opens, populated with the name and full path for the genotype data set generated by the HapMap Input Engine and the specified output folder, and runs.

The subset genotype data set is displayed in an .html file.

•	Map Data Set : This data set lists map data and other information for each of the SNPs in the study. Note : The SNPs are listed in rows in this data set.

Note : You can view the data in a file or data set by clicking either Open or View Subset (when the data set is very large).

General

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.