Process Description

OneMap Input Engine

The OneMap Import and Export Engine imports a text file in the format read by the OneMap R package (Margarido, de Souza, and Garcia 20071Margarido, G. R. A., Souza, A. P. and Garcia, A. A. F. (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144: 78-79.), and generates two SAS data sets:

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A data set that contains the marker genotypes and traits, and can be used as the Input Data Set for downstream JMP Genomics QTL mapping processes.

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A data set that lists marker map and other annotation information, and can be used as the Annotation Data Set for downstream JMP Genomics processes.

This process can also export information contained in a SAS data set and Annotation Data Set to a text file in the format read by the OneMap R package.

What do I need to import data from a OneMap-formatted txt file?

One .txt file is required to run the OneMap Input Engine. You should refer to the OneMap Tutorial found on the OneMap page at the Comprehensive R Archive Network (CRAN) for more information about this file. The SimuF1.txt file is located in the Sample Data\Genetics\QtlMapping directory included with JMP Genomics.

The SimuF1.txt file is shown below.

What do I need to export data to a OneMap-formatted txt file?

Two SAS data sets are required to run the OneMap Input Engine export process.

The first required data set is a SAS data set containing marker genotypes and traits. This must be a wide data set with samples in rows and markers in columns. The simuf1.sas7bdat data set is shown below:

The second data set is an Annotation Data Set that lists marker map or other annotation information. The simuf1_anno.sas7bdat annotation data set is shown below:

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the OneMap Input Engine output documentation for detailed descriptions.