Software (SAS, R-Project)

Software Available

Cucurbit Breeding Project

We have published articles describing software that may help in some research areas. The programs are written for SAS and R-Project, and are compatible with computer system that run those (Mac OS, MS-Windows, UNIX).

  • SASGene 1.2 (updated 3 March 1999)
    • SASGene is a SAS computer program for gene segregation and linkage analysis
      • Consists of 3 files written in the SAS macro language and one file with an example
      • Requires SAS version 6 or higher
      • Does single-gene goodness-of-fit testing, and analysis of gene linkage relationships
      • Calculates Chi-square, probability value and two-locus-combined phase for all gene pairs in segregation for the F2, BC1P1 and BC1P2 generations
    • SASGene developers
      • Jinsheng S. Liu (Visiting Scientist (China), Horticultural Science)
      • Todd C. Wehner (Professor, Horticultural Science)
      • Sandy B. Donaghy (SAS Consultant, Statistics)
    • Text versions of the SASGene files (SASGene 1.2 is the same as 1.1, except that linkage.sas was modified to correct a typographic error in the formula for calculating the SE for the F2 in coupling phase)
  • PathSAS 1.0 (updated 16 Jan 1998)
    • PathSAS is a SAS computer program for path analysis
      • Consists of 3 files written in the SAS macro language and one file with an example; also includes the Jackboot program
      • Requires SAS version 6 or higher
    • PathSAS developers
      • Christopher S. Cramer (Graduate Research Assistant, Horticultural Science)
      • Todd C. Wehner (Professor, Horticultural Science)
      • Sandy B. Donaghy (SAS Consultant, Statistics)
    • Corrections needed for SAS 8 and later
      • Change the variable name, intercep, to intercept. In the old version of SAS, variable names could only be 8 characters and SAS used the name intercep when it output datasets from PROC REG. In version 8, they changed the name of the variable to intercept since 9 characters are permitted.
    • Text versions of the PathSAS files for SAS version 9
    • Text version of the PathSAS file for SAS version 6
  • SASQuant 1.3 (updated 12 August 2008)
    • SASQuant is a SAS computer program for analysis of quantitative genetic data
      • Consists of 2 files written in the SAS macro language and one file with an example
      • Requires SAS version 8 or higher
      • Does quantitative genetic analysis of phenotypic data for populations (families) consisting of 6 generations (parents, F1, F2, BC1 to each parent)
      • Estimates genetic effects (Wright, Hayman mean separation analysis), generation variances, heritabilities, gain from selection, and number of effective factors
      • The J. Heredity article has a typo for calculation of aa, and shows EF5 calculated slightly differently (but correctly) from the SAS program. Those should be:
        • aa = -(4 x meanF2) + (2 x (meanBC1a + meanBC1b))
        • EF5 = (meanPb – meanPa)**2 / (8 x (varBC1a + varBC1b – (varF1 + 0.5 x varPa + 0.5 x varPb)))
    • SASQuant developers
      • Gabriele Gusmini (PepsiCo)
      • Todd C. Wehner (Horticultural Science, NC State Univ.)
      • Sandy B. Donaghy (Statistics, NC State Univ.)
    • Files for the SASQuant files
  • SASGxE 1.2 (updated 19 April 2016)
    • SASGxE developers
      • Mahendra Dia (Dupont Pioneer)
      • Todd C. Wehner (Horticultural Science, NC State Univ.)
      • Consuelo Arrelano (Statistics, NC State Univ.)
      • SASGxE is a SAS computer program for analysis of genotype by environment data
        • Consists of a file written in the SAS macro language (plus the instructions for use and the output log from SAS), a file with an example dataset (plus a template for the user’s data)
        • Requires SAS version 8 or higher
        • Useful for both genotype stability and location value
        • Estimates means, regression slopes and deviations for genotype vs. environmental index, Shukla’s stability ecovalence, and other useful stability statistics
      • Diagram of files for SASGxE (png)
      • Program for SASGxE (MSWord)
      • Files for SASGxE (zip with instructions, program, example data, example output)
      • Reference: Dia, M., T. C. Wehner, and C. Arellano. 2016. Analysis of genotype x environment interaction (GxE) using SAS programming. Agron. J. in press.
  • R-Project Program Versions
    • Get R-Project (free); install the main program (includes base, graphics, stats and other packages)
    • You may also want an R editor (free) for R-Project from RStudio
    • Training (free) for the use of R-Project is available from Quick-R
    • Available for Macintosh, Windows, Unix from servers around the world
  • rpathanalysis 1.1 (updated 4 November 2013)
    • rpathanalysis is an R-Project computer program for path analysis
        • Consists of files written in the R-Project language and one file with an example; also includes the Jackboot program
        • Requires pathanalysis, along with pls and boot
      • rpathanalysis developers
      • Reference: tbd
  • rgxe 1.1 (updated 17 March 2016)