STATISTICAL GENETICS Gene Mapping Through Linkage and Association

Examples from the book

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Example Scripts and Files

Merlin files from Chapter 8

sibs files .dat .map .ped

snp-scan files .dat .map .ped .clusters .clusters-only

Merlin files from Chapter 9

Keavney files .dat .map .ped

Merlin files and MX scripts from Chapter 10

ex_c2 files .dat .map .ped

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

X files .dat .map .ped

Xdummy files .dat .map .ped

imprint files .dat .map .ped

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

Chap15ex5 files .dat .ped

Chap15ex6 files .dat .ped

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

WHAP files from Chapter 18

candidate files .dat .map .ped