Examples from the book
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Example Scripts and Files
Merlin files from Chapter 8
snp-scan files .dat .map .ped .clusters .clusters-only
Merlin files from Chapter 9
Merlin files and MX scripts from Chapter 10
MX script for a univariate pi-hat QTL model
a2_1.mx (2.22 KB)
MX script for a univariate mixture distribution QTL model
a2_2.mx (2.29 KB)
MX script for a univariate pi-hat QTL model suitable for use with larger sibships
a2_3.mx (1.87 KB)
Merlin files and MX scripts from Chapter 11
MX script for a univariate imprinted QTL model
a2_4.mx (3.76 KB)
MX script for a univariate GxE QTL model
a2_5.mx (4.03 KB)
MX script for a univariate X chromosome QTL model
a2_6.mx (3.54 KB)
MX scripts from Chapter 12
MX script for the common factor QTL model
a2_7.mx (4.04 KB)
MX script for the Cholesky QTL model
a2_8.mx (3.82 KB)
MX script for the Longitudinal QTL model
a2_9.mx (4.54 KB)
QTDT files from Chapter 15
Example 1
Simulated data
PLINK files from Chapter 16
Since the publication of Statistical Genetics: Genemapping through linkage and association the amyotrophic lateral sclerosis and neurologically normal controls (Schymick et al., 2007) data sets that were used for the examples in Chapter 16 have been relocated. These data are no longer available from the Queue portal at the Coriell Institute (https://queue.coriell.org/q). They can now be obtained by applying for dbGaP access at the American National Institutes of Health (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap).
To assist readers who might find it difficult to gain access to the data, or need immediate access to a data set to learn how to use plink, we have created some simulated data based on the amyotrophic lateral sclerosis and neurologically normal controls (Schymick et al., 2007).
A pdf describing the simulated data and containing a revised version of the practicals is available here
The simulated data are available as four zip files:
case_map.zip
control_map.zip
case_pre.zip
control_pre.zip