qtlStats: Extract statistics from a QTL model

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

qtlStats Pushes a QTL model through fitqtl and calculates confidence intervals.

Usage

qtlStats(cross, mod, pheno.col, form = NULL, covar = NULL,
  calcConfint = TRUE, estEffects = TRUE, model = "normal", ...)

Arguments

cross	The qtl cross object with marker names that need to be changed.
mod	A QTL model, generated by either makeqtl (etc.) or stepwiseqtl.
pheno.col	Character or numeric vector of length 1, indicating the phenotype to be tested
form	If a generic (not stepwiseqtl) qtl model is supplied and does not contain a formula, this is required. The formula must match the QTL in the fitted QTL (mod) object.
covar	the covariate specified in the model / formula. See fitqtl.
calcConfint	Should confidence intervals be calculated? If so, see ... Also ensure that lodprofiles are included in the model.
estEffects	Should allelic effects be calculated?
model	Should a normal or binary model be fit?
...	additional arguments passed on to calcCis.

Details

A simple method to produce stats from a fitted model. Calls several R/qtl functions depending on the user specifications. These include fitqtl, summary.fitqtl, bayesint, dropint, and qtlTools::calcCis. The method of QTL inference is extracted from the QTL model.

Value

A dataframe of statistics.

Examples

library(qtlTools)
data(fake.bc)
cross<-fake.bc
cross <- calc.genoprob(cross, step=2.5)
mod <- makeqtl(cross, chr = c(2,5), pos = c(40,25), what = "prob")
nform <- "y ~ Q1 + Q2 + Q1*sex + sex"
sex <- data.frame(sex = cross$phe$sex)
mod <- refineqtl(cross, mod, pheno.col = "pheno1", qtl = mod,
   formula = nform, covar = sex, method="hk")
qtlStats(cross, pheno.col = "pheno1",form = nform, mod = mod, covar=sex)

data(fake.f2)
cross<-fake.f2
cross <- calc.genoprob(cross, step=2.5)
mod <- makeqtl(cross, chr = c(1,13), pos = c(27.5,27.5), what = "prob")
nform <- "y ~ Q1 + Q2 + Q1*sex + sex"
sex <- data.frame(sex = cross$phe$sex)
mod <- refineqtl(cross, mod, pheno.col = 1, qtl = mod,
   formula = nform, covar = sex, method="hk")
qtlStats(cross, pheno.col = 1,form = nform, mod = mod, covar=sex)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.