Casecontrol program is used to generate LINKAGE formatted pedigree files from case-control data and merge case-control data with other pedigrees and then you can analyze case-control data jointly with other data with pseudomarker or some other program.
Command is:
casecontrol
Input files are:
File structure for case.dat and control.dat is:
First line: number of markers in file
Column 1: Individual's ID { unique identifier
Column 2: Sex { 1 = Male, 2 = Female
Column 3+: Genetic data { marker phenotypes
Markers have to be in same order (and same number of them too) as in the pedigree file which you want to merge with case-control data.
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Case-Control v0.1 BETA - 11/06/2002
Program creates pre-makeped formatted LINKAGE pedigrees from case-control data
and merges them with other data. Done by Tero Hiekkalinna.
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Usage: casecontrol "pre-makeped pedigree file" [optional argument]
Input file argument:
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"pre-makeped pedigree file": Contains other pedigrees which you want merge with
case-control data.
optional agruments:
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n : Tells MAKEPED that there is no loops and all probands should be
chosen automatically.
Other input files:
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case.dat: Includes case data. First line number of markers. Next lines
case data with columns: personid, gender, marker1, marker2, etc.
controls.dat: Includes control data. First line number of markers. Next lines
case data with columns: personid, gender, marker1, marker2, etc.
Markers have to be in same order in all files. See readme.txt for more info.
Step-by-Step:
Use without loops:
casecontrol ped.pre n
Use without loops:
casecontrol ped.pre
and answer makeped questions.
Output files are:
Tero Hiekkalinna
http://www.helsinki.fi/~tsjuntun/pseudomarker/ ...and scroll down
Last update 28.5.2003