Running this process for the
example.gen
and the
example.sample
files generates the
Results
window shown below. Refer to the
Imputed SNP (Tall Format) Input Engine
process description for more information.
The
Results
window contains the following elements:
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Genotype Threshold Data Set:
This
wide
data set lists the most likely genotype for each marker, provided the value exceeds the specified
Genotype Probability Threshold
. Alternatively, for markers for which no genotype's probability meets the specified threshold, a
missing value
symbol (
.
) is listed.
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Expected Genotype Data Set
: This data set contains one column per
SNP
with the expected numeric genotype, where the genotype
2
represents
homozygous
for the
minor allele
, which is determined using the genotype probabilities. This data set can be used as the input to
SNP-Trait Association
with
Format of Marker Variables
set to
Numeric Genotypes
and only the
Trend
test selected to be performed.
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Genotype Probabilities Data Set
: This data set contains three columns per SNP with the probability for each genotype,
A/A
,
A/B
, and
B/B
. This data set is in
stacked
format grouped by SNP
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Annotation Data Set
: This data set lists on the information biological or chemical properties, such as gene identity or chromosomal location, for each of the markers/ molecular entities in the experiment. Refer to
Annotation Data Set
s for more information about this data set.
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Note
: You can view the data in a file or data set by clicking either
or
(when the data set is very large).
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Imputed SNP Trait Association
: Click
to launch the
Imputed SNP-Trait Association
process with the output data set specified as input.
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Click
to reopen the completed process dialog used to generate this output.
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Click
to close all graphics windows and underlying data sets associated with the output.
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