The OneMap Import and Export Engine imports a text file in the format read by the OneMap R package (Margarido, de Souza, and Garcia 2007
1
), and generates two SAS data sets:
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•
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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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|
•
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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.
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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.
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.
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 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
OneMap Input Engine
output documentation for detailed descriptions.