modify_qtl: Modify QTL model
In qtlpoly: Random-Effect Multiple QTL Mapping in Autopolyploids

Description Usage Arguments Value Author(s) References See Also Examples

Adds or removes QTL manually from a given model.

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, ...)

`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.
`...`	currently ignored

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.

Guilherme da Silva Pereira, gdasilv@ncsu.edu

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. doi: 10.1534/genetics.120.303080.

read_data, remim

  
  # Estimate conditional probabilities using mappoly package
  library(mappoly)
  library(qtlpoly)
  genoprob4x = lapply(maps4x[c(5)], calc_genoprob)
  data = read_data(ploidy = 4, geno.prob = genoprob4x, pheno = pheno4x, step = 1)

  # Search for QTL
  remim.mod = remim(data = data, pheno.col = 1, w.size = 15, sig.fwd = 0.0011493379,
sig.bwd = 0.0002284465, d.sint = 1.5, n.clusters = 1)

  # Modify model
  modified.mod = modify_qtl(model = remim.mod, pheno.col = 1, drop.qtl = 18)