The
Verify Gender of Samples
process determines genetic sex using the percentage of heterozygosity of
SNPs
on the X
chromosome
. Males that are observed to have a single
allele
from an X-linked SNP should have the
genotype
coded as
homozygous
for that allele. The output data set contains all of the
variables
from the
Input Data Set
plus three additional variables:
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GeneticSex
containing the genetically determined sex of each sample,
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HetPercent
containing the percentage of
heterozygous
SNPs on the X chromosome for each sample, and
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GenderError
reporting when there is a difference between the reported sex and genetically determined sex.
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One
Input Data Set
, containing all of the marker data, is required for this process. The sample data set used in the following example, the
morocco_snps1exp.sas7bdat
data set, represents the data from a study of gene
expression
variation and SNP
association
in southern Morocco (Idaghdour, Czika,
et al
., 2010).
Note
: The data was modified slightly to preserve anonymity of subjects.
A
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
morocco_anno.sas7bdat
annotation data set
is used in this example. 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 this process.
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
Verify Gender of Samples
output documentation for detailed descriptions and guides to interpreting your results.