mappoly (version 0.4.1)

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

Value

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

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)

Author

Marcelo Mollinari,

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.

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_. tools:::Rd_expr_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")