Sciences and methods > Biosciences > Programs > Pseudomarker
 
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Pseudomarker

Version

Version 1.0.5 is installed in HIPPU

Description

Pseudomarker can be used for joint linkage and LD analysis.

Usage

To initialize the program on HIPPU type:

module load pseudomarker


Pseudomarker needs pedigree file in a pre-makeped format. Map-file is in the format used by Mega2. Data file needs to be linkage formatted.

The basic call is:

pseudomarker -p pedigree.ped -m pedigree.map

Analysis options are appended after this basic call. For example, command:

pseudomarker -p pedigree.ped -m pedigree.map --dom

would run a dominant analysis.

All possible options are listed below. Further information is available on the developers site.

USAGE: 

   pseudomarker  [-p ] [-d ] [-m ] [-k]
                 [-f ] [--controlgt ] [--controlmap ] [--casegt ] 
                 [--casemap] [--ccphen] [--post] [--liabclass] [--rec]
                 [--prefix] [--dom] [--model] [--all] [--marker ]
                 [--phen] [--xlinked] [--forceloopbreak]
                 [--gemini] [--dpgs] [--lnlikematrix] [-g ]
                 [--verbose] [--mspause] [--] [-v] [-h]


Where: 

   -p ,  --pedigreefile 
     (value required)  Pedigree file

   -d ,  --datafile 
     (value required)  Linkage locus file

   -m ,  --mapfile (value required)  Marker map file

   -k ,  --modelfile 
     (value required)  Model file

   -f ,  --phenotypefile 
     (value required)  Phenotype file

   --controlgt 
     (value required)  Controls genotype file

   --controlmap (value required)  Controls marker map file

   --casegt 
     (value required)  Cases genotype file

   --casemap (value required)  Cases marker map file

   --ccphen 
     (value required)  Cases and controls phenotype name

   --post
     Pedigree file is in post-makeped format

   --liabclass
     Pedigree file has liability class

   --prefix 
     (value required)  Output file name prefix

   --dom
     Dominant pseudomarker analysis

   --rec
     Recessive pseudomarker analysis

   --model
     Model-based pseudomarker analysis

   --all
     Dominant, Recessive and Model-based pseudomarker analysis

   --marker 
     (value required)  Select specific marker

   --phen 
     (value required)  Select specific phenotype

   --xlinked
     X-linked data

   --forceloopbreak
     Force breaking of the loops

   --gemini
     Use GEMINI maximization routines (default is Direct Search)

   --dpgs
     Use D-prime grid search only for H2 and H3 starting values
     (Works with SNPs only)

   --lnlikematrix
     Write -2ln(likelihood) grid search matrix

   -g ,  --debug 
     (value required)  Debug program

   --verbose
     Verbose output

   --mspause
     Microsoft command prompt 'PAUSE' after analysis

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   -v,  --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

Manual

A tutorial for the program is available from the developers site.

Distribution

Binaries for Linux, Solaris and Windows can be acquired from the developers site.

User support

Saren Ari-Matti +358 9 457 2282 Ari-Matti.Saren at csc.fi