MIMQTL: QTL detection by MIM

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

QTL detection by MIM

Description

Perform QTL detection by multiple interval mapping

Usage

MIMQTL(
  cross,
  numeric.chr.format = FALSE,
  response.in.cross = TRUE,
  pheno.col = "y",
  response = NULL,
  method = "hk",
  geno.joinmap = NULL,
  phase = NULL,
  threshold = NA,
  nperm = 100,
  alpha = c(0.05, NA),
  plot = c(FALSE, FALSE),
  QTL_position = NULL,
  range_nb_qtl_max = seq(1:5),
  nrun = 10,
  additive.only = TRUE,
  p2d = "",
  scan2file = "",
  type.CI = "LOD-1",
  nb.cores = parallel::detectCores() - 2,
  verbose = 0
)

Arguments

cross	object
numeric.chr.format	logical to indicate if chromosome names are numeric
response.in.cross	logical to indicate if response studied is in cross$pheno, default is TRUE
pheno.col	character indicating column to study in cross$pheno
response	named numeric or vector for response if not in cross$pheno, default is NULL
method	method to detect QTL in qtl::scanone, default is "em"
geno.joinmap	genotypes at markers in the JoinMap format, if NULL (default), no estimation of allelic effects is given
phase	marker phases
threshold	genomewide significance LOD threshold, if NA (default), is found by permutations (with nperm parameter).
nperm	number of permutations to be done in qtl::scantwo, default is 100
alpha	vector of length 1 or 2 (optional) with thresholds for (1) the significance of QTL presence (based on permutations) and (2) the significance of linear regression on QTL effect, if NA, no threshold is applied and all allelic effects are kept.
plot	logical, default is FALSE.
QTL_position	matrix with genetic.distance and linkage.group as columns indicating QTL positions for plotting
range_nb_qtl_max	vector, default is seq(1:5)
nrun	integer, number of times to rerun qtl::stepwiseqtl
additive.only	logical, default is TRUE: no interaction between QTLs are added to the model
p2d	character, path to directory to save results
scan2file	optional path to scan2file (is added to p2d)
type.CI	type of confidence interval, default is "LOD-1"
nb.cores	number of cores
verbose	verbosity level (0/1/2)

Value

list of 3 elements: qtl.df is a data frame with QTL informations (linkage.group, position, LOD, interval.inf and interval.sup) / selected markers is a character vector for markers inside confidence interval /allelic effetcs is a data frame with a column predictor and a column effect with estimated allelic effects.

Author(s)

Agnes Doligez [aut], Charlotte Brault [ctbt], Timothee Flutre [ctb]

See Also

SIMQTL

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.