The
Marker Properties
process provides a convenient method for exploring several properties of all of the markers in a data set, for the purpose of
quality control
(QC) and possibly selecting markers to be removed from the analysis. This process calculates various single marker measures, such as marker informativeness and
allele
and
genotype
frequencies and tests for
Hardy-Weinberg equilibrium
(HWE), all using SAS PROC ALLELE. Output is displayed in an
.html
file, in charts, or both. Charts include plots of
p-values
versus physical location along the marker map and
cell plots
representing individual
genotypes
.
One
Input Data Set
is needed for this process. The
samplegmdata.sas7bdat
data set used in the following example was computer generated and consists of 1000 rows of individuals with 130 columns corresponding to data on these individuals. There are 2 categorical phenotypic
variables
(
sex
and
disease
status) and 4 quantitative phenotypic variables (
Qtrt1
,
Qtrt2
,
Qtrt3
, and
Qtrt4
). Genotypes for 60 different markers are presented in the two-column
allelic
format (
ma1
—
ma120
). This data set is partially shown below.
Note that this is a wide data set;
phenotypes
and markers are listed in columns, whereas individuals are listed in rows.
The second, optional, data set is the
Annotation Data Set
. This data set contains information, such as gene identity or chromosomal location, for each of the markers. The
annotation data set
used in this example, the
samplemap
data set, was computer generated and identifies markers, location and gene identities. A portion of this data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.
Note
: The top-to-bottom order of the rows in the annotation data set matches the left-to-right order of the columns in the input data set. This correspondence is required for markers to be matched appropriately.
Both data sets are
described in
Data Sets Used in JMP Genomics Processes
and
are included in the
Sample Data
folder.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The output generated by this process is summarized in a Tabbed report. Refer to the
Marker Properties
output documentation for detailed descriptions and guides to interpreting your results.