qtlpoly (version 0.2.4)

feim: Fixed-effect interval mapping (FEIM)

Description

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

Usage

feim(
  data = data,
  pheno.col = NULL,
  w.size = 15,
  sig.lod = 7,
  d.sint = 1.5,
  plot = NULL,
  verbose = TRUE
)
# S3 method for qtlpoly.feim
print(x, pheno.col = NULL, sint = NULL, ...)

Value

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.

Arguments

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.

...

currently ignored

Author

Guilherme da Silva Pereira,

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. tools:::Rd_expr_doi("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.

See Also

permutations

Examples

  # 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 = 5)

  # Perform remim
  feim.mod = feim(data = data, sig.lod = 7)