modify_qtl: Modify QTL model

In guilherme-pereira/QTLpoly: Random-effect multiple QTL mapping in autopolyploids

Description

Adds or removes QTL manually from a given model.

Usage

modify_qtl(
  model,
  pheno.col = NULL,
  add.qtl = NULL,
  drop.qtl = NULL,
  verbose = TRUE
)

## S3 method for class 'qtlpoly.modify'
print(x, pheno.col = NULL)

Arguments

model	an object of class qtlpoly.model containing the QTL to be modified.
pheno.col	a phenotype column number whose model will be modified or printed.
add.qtl	a marker position number to be added.
drop.qtl	a marker position number to be removed.
verbose	if TRUE (default), current progress is shown; if FALSE, no output is produced.
x	an object of class qtlpoly.modify to be printed.

Value

An object of class qtlpoly.modify which contains a list of results for each trait with the following components:

pheno.col	a phenotype column number.
stat	a vector containing values from score statistics.
pval	a vector containing p-values from score statistics.
qtls	a data frame with information from the mapped QTL.

Author(s)

Guilherme da Silva Pereira, [e-mail]

References

Pereira GS, Gemenet DC, Mollinari M, Olukolu BA, Wood JC, Mosquera V, Gruneberg WJ, Khan A, Buell CR, Yencho GC, Zeng ZB (2020) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population, Genetics 215 (3): 579-595. http://doi.org/10.1534/genetics.120.303080.

See Also

read_data, remim

Examples

  ## Not run: 
  # load raw data
  data(maps)
  data(pheno)

  # estimate conditional probabilities using mappoly package
  library(mappoly)
  genoprob <- lapply(maps, calc_genoprob)

  # prepare data
  data <- read_data(ploidy = 6, geno.prob = genoprob, pheno = pheno, step = 1)

  # perform remim
  remim.mod <- remim(data = data, w.size = 15, sig.fwd = 0.01, sig.bwd = 0.0001,
    d.sint = 1.5, n.clusters = 4, plot = "remim")

  # modify model
  modified.mod <- modify_qtl(model = remim.mod, pheno.col = 3, add.qtl = 184)
  
## End(Not run)

guilherme-pereira/QTLpoly documentation built on Oct. 10, 2021, 10:22 p.m.