get_qtl_intervals: Get list of QTL intervals.

In gact/utl: Utility Functions for R/qtl Analysis

Description

Given a specified LOD threshold and associated significance level alpha, this function gets a list of approximate QTL intervals for an R/qtl scanone object.

Usage

get_qtl_intervals(
  x,
  chr = NULL,
  lodcolumn = NULL,
  threshold = NULL,
  ci.function = c("lodint", "bayesint"),
  drop = 1.5,
  prob = 0.95,
  expandtomarkers = FALSE
)

Arguments

x	An R/qtl scanone object.
chr	Vector indicating which sequences to consider. If no sequences are specified, the QTL interval list is created with respect to every sequence in x.
lodcolumn	This parameter indicates which LOD column to consider. This must be either a LOD column name or an index with respect to the set of LOD columns. If no LOD column is specified and one such column is found, that column is used by default; otherwise a LOD column must be specified.
threshold	A single numeric LOD significance threshold, or a summary.scanoneperm object containing one such threshold and its associated significance level.
ci.function	Option to indicate which R/qtl function should be used for estimating approximate confidence intervals for QTL location. Set to 'lodint' for LOD support intervals (adjusting stringency with the drop parameter), or to 'bayesint' for Bayesian credible intervals (adjusting stringency with the prob parameter). For more information on the QTL interval methods used, see functions lodint and bayesint in the R/qtl manual, as well as Section 4.5 of Broman and Sen (2009).
drop	LOD units that the LOD profile must drop to form the interval. This is used only if ci.function is set to 'lodint'.
prob	Desired probability coverage for the Bayesian credible interval. This is used only if ci.function is set to 'bayesint'.
expandtomarkers	Expand the LOD interval to the nearest flanking markers, or to the respective terminal loci.

Value

A list of data.frame objects, each containing three rows of information about the lower interval limit, peak, and upper interval limit (respectively) of a QTL. Returns an empty list if there are no significant QTLs.

Author(s)

Thomas A. Walsh

Yue Hu

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)

Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl. New York: Springer. (Website)

See Also

R/qtl website

Examples

## Not run: 
# Load R/qtl hyper dataset.
data(hyper, package='qtl')

# Estimate genetic map of hyper data.
gmap <- qtl::est.map(hyper, offset=0.0)

# Set newly estimated genetic map.
hyper <- qtl::replace.map(hyper, gmap)

# Calculate genotype probabilities.
hyper <- qtl::calc.genoprob(hyper, step=1.0)

# Do single-QTL analysis.
scanone.result <- qtl::scanone(hyper, pheno='bp')

# Do single-QTL permutation analysis.
scanone.perms <- qtl::scanone(hyper, pheno='bp', n.perm=1000L)

# Get LOD threshold values from single-QTL permutation results.
threshold.vals <- summary(scanone.perms, alpha=0.05)

# Get LOD threshold value for first LOD column.
threshold.val <- qtl:::subset.scanoneperm(threshold.vals, lodcolumn=1L)

# Get QTL intervals for first LOD column.
qtl.intervals <- get_qtl_intervals(scanone.result, lodcolumn=1L, threshold=threshold.val,
                                   ci.function='bayesint')

## End(Not run)

gact/utl documentation built on June 1, 2021, 4:24 p.m.