import_data_from_polymapR: Import data from polymapR

Description

Function to import datasets from polymapR.

Usage

import_data_from_polymapR(
  input.data,
  ploidy,
  parent1 = "P1",
  parent2 = "P2",
  input.type = c("discrete", "probabilistic"),
  prob.thres = 0.95,
  pardose = NULL,
  offspring = NULL,
  filter.non.conforming = TRUE,
  verbose = TRUE
)

Arguments

input.data: a polymapR dataset
ploidy: the ploidy level
parent1: a character string containing the name (or pattern of genotype IDs) of parent 1
parent2: a character string containing the name (or pattern of genotype IDs) of parent 2
input.type: Indicates whether the input is discrete ("disc") or probabilistic ("prob")
prob.thres: threshold probability to assign a dosage to offspring. If the probability is smaller than thresh.parent.geno, the data point is converted to 'NA'.
pardose: matrix of dimensions (n.mrk x 3) containing the name of the markers in the first column, and the dosage of parents 1 and 2 in columns 2 and 3. (see polymapR vignette)
offspring: a character string containing the name (or pattern of genotype IDs) of the offspring individuals. If NULL (default) it considers all individuals as offsprings, except parent1 and parent2.
filter.non.conforming: if TRUE exclude samples with non expected genotypes under no double reduction. Since markers were already filtered in polymapR, the default is FALSE.
verbose: if TRUE (default), the current progress is shown; if FALSE, no output is produced

Author

Marcelo Mollinari mmollin@ncsu.edu

Details

See examples at https://rpubs.com/mmollin/tetra_mappoly_vignette.

References

Bourke PM et al: (2019) PolymapR — linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496–3502. tools:::Rd_expr_doi("10.1093/bioinformatics/bty1002")

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")