Software for distribution

(last updated: July 19, 2006) (News) (back)


General info:
  • All software listed here are SAS macros, so you need to have access to SAS software (SAS Institute Inc.).
  • Extraction of .zip-Files: Under Windows NT, WinZip can be used to extract the files. Under Unix, the files can be extracted by the command    unzip -aa <filename>
  • Documentation: Each .zip-file contains a .ps-file (Postscript) and/or a .pdf-file (Acrobat Reader), which explains the usage of the macro.
  • If you encounter any problems or if you have any other comment, please send me email
  • All software is free of charge, but there is ABSOLUTELY NO WARRANTY!
RC-TDT:
(Version 1.1d,
 July 17, 2006)
  • Description:
    The reconstruction-combined transmission disequilibrium test (RC-TDT, Knapp 1999a) is a family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. rctdt.zip (84.269 Bytes) contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values (Knapp 1999b).
  • References:
    Knapp M (1999a): The transmission/disequilibrium test and parental-genotype reconstruction: the reconstruction-combined transmission/disequilibrium test. American Journal of Human Genetics 64, 861-870. (PDF)
    Knapp M (1999b): Using exact P values to compare the power between the reconstruction-combined transmission/disequilibrium test and the sib transmission/disequilibrium test. American Journal of Human Genetics 65, 1208-1210.
    Horvath S, Laird NM, Knapp M (2000): The transmission/disequilibrium test and parental-genotype reconstruction for X-chromosomal markers. American Journal of Human Genetics 66, 1161-1167.
TDTPOWER:
(Version 1.0b,
 Aug 8, 2001)
  • Description:
    tdtpower.zip (44.988 Bytes) contains an SAS macro that calculates the sample size required for obtaining a prescribed power against a specified alternative for the transmission/disequilibrium test (TDT; Spielman et al. 1993). The sample size calculation is based on a power approximation for the TDT which has been described by Knapp (1999). The SAS macro allows to calculate sample sizes even if (i) there is no complete linkage disequilibrium between the alleles at the marker and the disease locus; (ii) the recombination fraction between marker and disease locus is greater than 0; and (iii) the families are ascertained not only according to the presence of a certain number of affected children, but also according to the presence of a certain number of unaffected children.
  • References:
    Knapp M (1999): A note on power approximations for the transmission/disequilibrium test. American Journal of Human Genetics 64, 1177-1185. (PDF)
    Spielman RS, McGinnis RE, Ewens WJ (1993): Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). American Journal of Human Genetics 52, 506-516.
ILR:
(Version 2.2,
Nov 18, 2005)
  • Description:
    ilr.zip (211.396 Bytes) contains an SAS macro that calculates the statistic of the restricted likelihood-ratio ASP test allowing for imprinting.
  • Reference:
    Knapp M, Strauch K (2004): Affected-sib-pair test for linkage based on constraints for identical-by-descent distributions corresponding to disease models with imprinting. Genetic Epidemiology 26, 273-285. (Erratum: 28, 288)
HOTEL_CC:
(Version 0.1,
 Sep 17, 2003)
  • Description:
    hotel_cc.zip (153.500 Bytes) contains an SAS macro that calculates Hotelling's T2 statistic for case-control data.
  • Reference:
    Fan R, Knapp M (2003): Genome association studies of complex diseases by case-control designs. American Journal of Human Genetics 72, 850-868.
HOTEL_FAM:
(Version 0.3,
 July 19, 2006)
  • Description:
    hotel_fam.zip (170.767 Bytes) contains an SAS macro that calculates Hotelling's T2 statistic for data of nuclear families with a single affected child.
  • Reference:
    Fan R, Knapp M, Wjst M, Zhao C, Xiong M (2005): High resolution T2 association tests of complex diseases based on family data. Annals of Human Genetics 69, 1-22.
FAMHAP:
(Version 12,
 May 24, 2004)
  • Description:
    FAMHAP is a program written in C for maximum-likelihood estimation of haplotype frequencies in nuclear families, which can be obtained from Tim Becker's website.
  • References:
    Becker T, Knapp M (2004): Maimum-likelihood estimation of haplotype frequencies in nuclear families. Genetic Epidemiology 27: 21-32.
    Becker T, Knapp M (2004): A powerful strategy to account for multiple testing in the context of haplotype analysis. American Journal of Human Genetics 75, 561-570.
Miscellaneous:
  • exdmlb.zip (32.255 Bytes, Version 1.0, Jul 17, 2000) contains an SAS macro that calculates exact critical values for the disequilibrium-maximum-likelihood-binomial test (DMLB; Huang and Jiang 1999).
    References:
    Horvath S, Windemuth C, Knapp M (2000): The disequilibrium maximum-likelihood-binomial test does not replace the transmission/disequilibrium test. American Journal of Human Genetics 67, 531-534.
    Huang J, Jiang Y (1999): Linkage detection adaptive to linkage disequilibrium: the disequilibrium-likelihood-binomial test for affected-sibship data. American Journal of Human Genetics 65, 1741-1759.