rf_list_to_matrix: Recombination fraction list to matrix

In mappoly: Genetic Linkage Maps in Autopolyploids

Recombination fraction list to matrix

Description

Transforms the recombination fraction list contained in an object of class mappoly.twopt or mappoly.twopt2 into a recombination fraction matrix

Usage

rf_list_to_matrix(
  input.twopt,
  thresh.LOD.ph = 0,
  thresh.LOD.rf = 0,
  thresh.rf = 0.5,
  ncpus = 1L,
  shared.alleles = FALSE,
  verbose = TRUE
)

## S3 method for class 'mappoly.rf.matrix'
print(x, ...)

## S3 method for class 'mappoly.rf.matrix'
plot(
  x,
  type = c("rf", "lod"),
  ord = NULL,
  rem = NULL,
  main.text = NULL,
  index = FALSE,
  fact = 1,
  ...
)

Arguments

input.twopt	an object of class mappoly.twopt or mappoly.twopt2
thresh.LOD.ph	LOD score threshold for linkage phase configurations (default = 0)
thresh.LOD.rf	LOD score threshold for recombination fractions (default = 0)
thresh.rf	the threshold used for recombination fraction filtering (default = 0.5)
ncpus	number of parallel processes (i.e. cores) to spawn (default = 1)
shared.alleles	if TRUE, computes two matrices (for both parents) indicating the number of homologues that share alleles (default = FALSE)
verbose	if TRUE (default), current progress is shown; if FALSE, no output is produced
x	an object of class mappoly.rf.matrix
...	currently ignored
type	type of matrix that should be printed. Can be one of the following: "rf", for recombination fraction or "lod" for LOD Score
ord	the order in which the markers should be plotted (default = NULL)
rem	which markers should be removed from the heatmap (default = NULL)
main.text	a character string as the title of the heatmap (default = NULL)
index	logical should the name of the markers be printed in the diagonal of the heatmap? (default = FALSE)
fact	positive integer. factor expressed as number of cells to be aggregated (default = 1, no aggregation)

Details

thresh_LOD_ph should be set in order to only select recombination fractions that have LOD scores associated to the linkage phase configuration higher than thresh_LOD_ph when compared to the second most likely linkage phase configuration.

Value

A list containing two matrices. The first one contains the filtered recombination fraction and the second one contains the information matrix

Author(s)

Marcelo Mollinari, [e-mail]

References

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Examples

    all.mrk <- make_seq_mappoly(hexafake, 1:20)
    red.mrk <- elim_redundant(all.mrk)
    unique.mrks <- make_seq_mappoly(red.mrk)
    all.pairs <- est_pairwise_rf(input.seq = unique.mrks,
                               ncpus = 1,
                               verbose = TRUE)

    ## Full recombination fraction matrix
    mat.full <- rf_list_to_matrix(input.twopt = all.pairs)
    plot(mat.full)
    plot(mat.full, type = "lod")
 

mappoly documentation built on Jan. 6, 2023, 1:16 a.m.