Ellen M. Wijsman: Software and data

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• New November 12, 2009: Kinship
• Coming very soon: software to integrate the results from Kinship with genome-wide case-control testing. A little documentation just needs to be completed.
• Kinship and README file: Software to carry out computations to estimate kinship coefficients for case-control analyses in the presence of cryptic relatedness, as described in the paper: Choi et al (2009) "Case-control association testing in the presence of unknown relationships" Genetic Epidemiology (in press), online March 30, 2009.
• PANGAEA for the MORGAN package or Loki
• lnkg2lmm: A Perl script to convert linkage-style files to MORGAN-lm_markers-style files, also distributed from the PANGAEA/MORGAN distribution site.
  Two sets of example files include a binary trait, and a quantitative trait , both based on a couple of simulated data sets from the paper by Wijsman et al (2006) AJHG 79:846-858.
• Perl scripts for Loki: additional useful scripts for manipulating files from Loki are provided as-is. These are scripts that members of my group have written and that carry out commonly-used tasks. These scripts include computation of Bayes Factors for linkage by uniform intervals or by inter-marker intervals (different from the L-score distributed with Loki); flipping of QTL models to eliminate the model bimodality that is intrinsic in the analysis approach; extracting QTL models that meet particular conditions; and extracting QTL models that fall in an ellipse in a heterozygote-homozygote effect scatter plot. See beginning of each perl script for program documentation.
• SimSuite Ver. 1.0 Scripts, README file, and Examples: A suite of Perl scripts to manage trait simulation from Loki output files, marker simulation, and analysis of results with Loki and/or SOLAR, described by Igo & Wijsman (2008) Empirical significance values for linkage analysis: trait simulation using posterior model distributions from MCMC oligogenic segregation analysis. Genetic Epidemiology 32:119-131.
• Simulated data used in the paper by Wijsman et al (2006) AJHG 79:846-858 is available at the PANGAEA distribution site.
• Other programs are currently distributed informally, and in a state that is "as is". Contact me if you are interested.