An
Annotation Group Plots
tab is shown below:
The
Annotation Group Results
tab contains the following elements:
|
•
|
One or more
P
-Value Plots.
|
When there are multiple annotation groups, there is a separate
Annotation Group Results
tab for each annotation group. In this example there are two annotation groups,
CandGene 1
and
CandGene 2
. The
CandGene 1 Results
tab is shown above.
This tab contains one or more
p-value
plots. The
y
-axis
variable
is the
p
-value from the HWE test, converted to the
-log
or
-log
10
scale if selected in the process
dialog
. The
x
-axis plots location of the marker according to the annotation location variable within the annotation group. A horizontal reference line is drawn as a red, dashed line at the significance level that was specified. For
-log
- or
-log
10
-converted
p
-values, markers above this line are significant; for
p
-values on the original scale, markers below the line are significant.
For the given annotation group, the
distribution
of MAF and missing
genotype
proportion across the markers in the annotation group are displayed, using histograms and
quantile
information.
These results can give guidance on values to set for the
Filters for Markers cutoffs to be used to filter markers/individuals
in the
Action Buttons
pane.