mappoly (version 0.2.3)

import_from_updog: Import from updog

Description

Read objects with information related to genotype calling in polyploids. Currently this function supports output objects created with the updog (output of multidog function) package. This function creates an object of class mappoly.data

Usage

import_from_updog(
  object,
  prob.thres = NULL,
  filter.non.conforming = FALSE,
  verbose = TRUE
)

Arguments

object

the name of the object of class multidog

prob.thres

probability threshold to associate a marker call to a dosage. Markers with maximum genotype probability smaller than 'prob.thres' are considered as missing data for the dosage calling purposes

filter.non.conforming

if TRUE (default) exclude samples with non expected genotypes under random chromosome pairing and no double reduction

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

Value

An object of class mappoly.data which contains a list with the following components:

m

ploidy level

n.ind

number individuals

n.mrk

total number of markers

ind.names

the names of the individuals

mrk.names

the names of the markers

dosage.p

a vector containing the dosage in parent P for all n.mrk markers

dosage.q

a vector containing the dosage in parent Q for all n.mrk markers

sequence

a vector indicating which sequence each marker belongs. Zero indicates that the marker was not assigned to any sequence

sequence.pos

physical position of the markers into the sequence

prob.thres

probability threshold to associate a marker call to a dosage. Markers with maximum genotype probability smaller than 'prob.thres' were considered as missing data in the 'geno.dose' matrix

geno.dose

a matrix containing the dosage for each markers (rows) for each individual (columns). Missing data are represented by ploidy_level + 1

geno

a data.frame containing the probability distribution for each combination of marker and offspring. The first two columns represent the marker and the offspring, respectively. The remaining elements represent the probability associated to each one of the possible dosages. Missing data are converted from NA to the expected segregation ratio using function segreg_poly

n.phen

number of phenotypic traits

phen

a matrix containing the phenotypic data. The rows correspond to the traits and the columns correspond to the individuals

chisq.pval

a vector containing p-values related to the chi-squared test of Mendelian segregation performed for all markers

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_. 10.1534/g3.119.400378

Examples

# NOT RUN {
if(requireNamespace("updog", quietly = TRUE)){
library("updog")
data("uitdewilligen")
mout = multidog(refmat = t(uitdewilligen$refmat), 
                sizemat = t(uitdewilligen$sizemat), 
                ploidy = uitdewilligen$ploidy, 
                model = "f1",
                p1_id = colnames(t(uitdewilligen$sizemat))[1],
                p2_id = colnames(t(uitdewilligen$sizemat))[2],
                nc = 2)
mydata = import_from_updog(mout)
mydata
plot(mydata)
}
# }
# NOT RUN {
# }