feim: Fixed-effect interval mapping (FEIM)
In guilherme-pereira/QTLpoly: Random-effect multiple QTL mapping in autopolyploids

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

Performs interval mapping using the single-QTL, fixed-effect model proposed by Hackett et al. (2001).

feim(
  data = data,
  pheno.col = NULL,
  w.size = 15,
  sig.lod = 7,
  d.sint = 1.5,
  plot = "feim",
  verbose = TRUE
)

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

`data`	an object of class `qtlpoly.data`.
`pheno.col`	a numeric vector with the phenotype columns to be analyzed; if `NULL` (default), all phenotypes from `'data'` will be included.
`w.size`	a number representing the window size (in centiMorgans) to be avoided on either side of QTL already in the model when looking for a new QTL, e.g. 15 (default).
`sig.lod`	the vector of desired significance LOD thresholds (usually permutation-based) for declaring a QTL for each trait, e.g. 5 (default); if a single value is provided, the same LOD threshold will be applied to all traits.
`d.sint`	a d value to subtract from logarithm of the odds (LOD-d) for support interval calculation, e.g. d=1.5 (default) represents approximate 95% support interval.
`plot`	a suffix for the file's name containing plots of every algorithm step, e.g. "remim" (default); if `NULL`, no file is produced.
`verbose`	if `TRUE` (default), current progress is shown; if `FALSE`, no output is produced.
`x`	an object of class `qtlpoly.feim` to be printed.
`sint`	whether `"upper"` or `"lower"` support intervals should be printed; if `NULL` (default), QTL peak information will be printed.

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

`pheno.col`	a phenotype column number.
`LRT`	a vector containing LRT values.
`LOD`	a vector containing LOD scores.
`AdjR2`	a vector containing adjusted R^2.
`qtls`	a data frame with information from the mapped QTL.
`lower`	a data frame with information from the lower support interval of mapped QTL.
`upper`	a data frame with information from the upper support interval of 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. http://doi.org/10.1534/genetics.120.303080.

Hackett CA, Bradshaw JE, McNicol JW (2001) Interval mapping of quantitative trait loci in autotetraploid species, Genetics 159: 1819-1832. http://www.genetics.org/content/159/4/1819

permutations

  ## 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
  feim.mod <- feim(data = data, sig.lod = 7, plot = "feim")
  
## End(Not run)