onemap (version 2.0-4)

try.seq: Try to map a marker into every possible position between markers

Description

For a given linkage map and an additional unpositioned marker, this function estimates parameters for all possible maps including the new marker, while keeping the original linkage map unaltered.

Usage

try.seq(input.seq, mrk, tol=10E-2, draw.try=FALSE, pos=NULL, verbose=FALSE)
# S3 method for try
print(x,j=NULL, …)

Arguments

input.seq

an object of class sequence with a predefined order.

mrk

the index of the marker to be tried, according to the input file.

tol

tolerance for the C routine, i.e., the value used to evaluate convergence.

draw.try

if TRUE, a diagnostic graphic is displayed. See Details section.

pos

defines in which position the new marker mrk should be placed for the diagnostic graphic. If NULL (default), the marker is placed on the best position i.e. the one which results LOD = 0.00

verbose

if FALSE (default), simplified output is displayed. if TRUE, detailed output is displayed.

x

an object of class try.

j

if NULL (default), output is a summary of the results for all possible positions of the additional marker. Otherwise, an integer makes detailed output to be printed for the corresponding position. This integer must be less than or equal to the length of the original sequence plus 1.

…

further arguments, passed to other methods. Currently ignored.

Value

An object of class try, which is a list containing the following components:

ord

a list containing results for every linkage map estimated. These results include linkage phases, recombination frequencies and log-likelihoods.

LOD

a vector with LOD-Scores for each position where the additional marker is placed. This Score is based on the best combination of linkage phases for each map.

try.ord

a matrix with the orders of all linkage maps.

data.name

name of the object of class outcross with the raw data.

twopt

name of the object of class rf.2pts with the 2-point analyses.

Details

The diagnostic graphic is made of three figures: i) the top figure represents the new genetic map obtained with the insertion of the new marker mrk on position pos. If pos = NULL (default), the marker is placed on the best position i.e. the one which results LOD = 0.00, which is indicated by a red triangle; ii) the left bottom figure represents the base map (contained in input.seq) on x-axis and the LOD-Scores of the linkage maps obtained with the new marker mrk tested at the beginning, between and at the end of the base map. Actually, it is a graphic representation of the LOD vector (see Value section). The red triangle indicates the best position where the new marker mrk should be placed; iii) the right bottom figure is the non-interactive rf.graph.table function for the new genetic map. It plots a matrix of pairwise recombination fractions (under the diagonal) and LOD Scores (upper the diagonal) using a color scale.

References

Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43

Jiang, C. and Zeng, Z.-B. (1997). Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.

Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E. and Newburg, L. (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.

Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetic maps. Heredity 103: 494-502

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

Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences. Genetical Research 79: 85-96

See Also

make.seq and compare.

Examples

# NOT RUN {
  #outcrossing example
  data(example.out)
  twopt <- rf.2pts(example.out)
  markers <- make.seq(twopt,c(2,3,12,14))
  markers.comp <- compare(markers)
  base.map <- make.seq(markers.comp,1)

  extend.map <- try.seq(base.map,30)
  extend.map
  print(extend.map,5) # best position
  print(extend.map,4) # second best position

  #F2 example
  data(fake.f2.onemap)
  twopt <- rf.2pts(fake.f2.onemap)
  all.mark <- make.seq(twopt,"all")
  groups <- group(all.mark)
  LG3 <- make.seq(groups,3)
  LG3.ord <- order.seq(LG3, subset.search = "twopt", twopt.alg = "rcd", touchdown=TRUE)
  LG3.ord
  safe.map<-make.seq(LG3.ord,"safe") 
  extend.map <- try.seq(safe.map,64)
  extend.map
  (new.map<-make.seq(extend.map,14)) # best position

  #Display diagnostic graphics
  try.seq(safe.map,64,draw.try=TRUE) #best position (default)
  try.seq(safe.map,64,draw.try=TRUE,pos=13) #second best position
  try.seq(safe.map,64,draw.try=TRUE,pos=4) #wrong position

  #Trying to position an unliked marker
  try.seq(safe.map,66,draw.try=TRUE) #note the inconsistencies in the graphic

# }