rf_2pts function

Two-point analysis between genetic markers

Performs the two-point (pairwise) analysis proposed by Wu et al. (2002) between all pairs of markers.

rf_2pts(input.obj, LOD = 3, max.rf = 0.5, verbose = TRUE, rm_mks = FALSE)

Arguments

• input.obj: an object of class onemap.
• LOD: minimum LOD Score to declare linkage (defaults to 3).
• max.rf: maximum recombination fraction to declare linkage (defaults to 0.50).
• verbose: logical. If TRUE, current progress is shown; if FALSE, no output is produced.
• rm_mks: logical. If TRUE the algorithm will remove the markers for which it found numerical problems to calculates the recombination fraction. The numerical problems can happens because of excess of missing data or segregation deviation.

Returns

An object of class rf_2pts, which is a list containing the following components: - n.mar: total number of markers. - LOD: minimum LOD Score to declare linkage. - max.rf: maximum recombination fraction to declare linkage.

• input: the name of the input file. - analysis: an array with the complete results of the two-point analysis for each pair of markers.

Details

For n markers, there are

pairs of markers to be analyzed. Therefore, completion of the two-point analyses can take a long time.

Note

The thresholds used for LOD and max.rf will be used in subsequent analyses, but can be overriden.

Examples

data(onemap_example_out)

  twopts <- rf_2pts(onemap_example_out,LOD=3,max.rf=0.5) # perform two-point analyses
  twopts

  print(twopts,c("M1","M2")) # detailed results for markers 1 and 2

References

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

Author(s)

Gabriel R A Margarido gramarga@gmail.com and Marcelo Mollinari mmollina@usp.br