rf_2pts {onemap}

Two-point analysis between genetic markers

Description

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

Usage

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.

Details

For n markers, there are

\frac{n(n-1)}{2}

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

Value

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.

Note

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

Author(s)

Gabriel R A Margarido [e-mail] and Marcelo Mollinari [e-mail]

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.

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