The
Basic Linkage Mapping Workflow
process builds and runs a
workflow
to create a genetic
linkage
map using marker
genotypes
for individuals or lines from an experimental inbred
population
. This automated process runs the
Recombination and Linkage Groups
,
Linkage Map Order
,
Linkage Map Viewer
, and
Subset and Reorder Genetic Data
processes to perform the following analyses:
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1
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Compute recombination frequencies between all pairs of markers, test for marker segregation distortion, and assign markers into linkage groups using automated Hierarchical Clustering (this algorithm is used by default if a
framework map
has
not
been specified) or Minimum Recombination Grouping (this algorithm is used when a
framework map
is
used to accommodate the constraints of markers in known groups).
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2
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Run the Map Order optimization algorithm to determine the optimal order of the markers within the generated linkage groups and compute the
genetic distance
map based on the pairwise recombination frequencies.
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4
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An
Input Genotype SAS Data Set
is
required
for this process. The
qtlsfsample_geno.sas7bdat
data set serves as an example, and is shown below. It contains 300 rows of individuals and 40 columns corresponding to identifier,
trait
, and marker genotype information.
Optional
data sets include:
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•
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An
Annotation SAS Data Set
. This data set contains information such as gene identity or chromosomal location, for each of the markers. The
qtlsfsample_anno.sas7bdat
data set serves as an example, and is shown below. It contains 36 rows of markers and 4 columns containing
chromosome
, marker, and positioning information.
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•
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A
Framework Map Data Set
. This data set can be used to create linkage groups for markers in the genotype data that incorporate prior knowledge of markers that already belong to pre-defined groups. The
qtlbcsample_frame.sas7bdat
data set serves as an example, and is shown below.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
When you click
, the
Basic Linkage Mapping Workflow
process begins by opening the
Workflow Builder
. The
Workflow Builder
builds a
settings file
for each process, containing the information from the data sets and parameters specified in the
Basic Linkage Mapping Workflow
dialog
. Once the setting files are generated and saved, the individual processes in the workflow are sequentially opened, populated, and run. The results of the processes are saved in the specified output folder. Finally, a JMP
journal
, providing links to the workflow dialog and the results of each process, is generated.
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Click
.
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The
Workflow Builder
dialog shows the settings for each of the processes in the workflow. You can select and edit individual settings to adjust your analysis by highlighting the desired workflow and selecting
.
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Clicking each of the
buttons on the journal brings up the output for each of the processes. This enables you to examine each set of output so that adjustments can be made to the individual settings, as needed. For your convenience, links to default
Basic Linkage Mapping Workflow
processes are given below.
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