Newport iServer MicroServer iTHX-M, Operator'S Manual

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Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
Quantitative Traits
The GeneHunter open source software datafile contains the means and
covariances for the traits. Dummy values are written by the
application. The user has to edit the file with the correct values.
Allele Frequencies
The allele frequencies are read in from the Freq A Call NetAffx
™
annotation file. If this annotation file is not available, the frequencies
are set to 0.5.
GeneHunter Open Source Software Recombination Rates
The recombination rates are calculated from the Genetic Map
positions in the GTYPE file. The genetic distance is the difference
between current and following SNPs. The genetic distance is
converted to recombination rate, using the Haldane map function
where d is the genetic distance between two markers in centiMorgans.
EXPORTING DATA IN TAB-DELIMITED FORMAT
To export SNP data in tab-delimited format:
1.
Click the SNP Export button in the Genotyping Views
shortcut bar, or select Tools SNP Export... from the menu bar.
The SNP Export dialog box opens (Figure 6.42) .
2.
Click the Tab Delimited tab to select the export format.
θ
θ
1
2
---
1
2 d
100
--------- –
⎝ ⎠
⎛ ⎞
exp – =
GTYPE_manual.book Page 230 Wednesday, August 2, 2006 11:31 AM