getQTLIntervals: Get QTL intervals.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Value Author(s) References See Also

Given a specified LOD threshold and associated significance level alpha (or alternatively, false-discovery rate fdr), this function gets approximate QTL intervals for a given scanone object, or a qtl object with a 'lodprofile' attribute (as output by R/qtl function refineqtl).

## Generic method.
getQTLIntervals(x, chr=NULL, ci.function=c('lodint', 'bayesint'), drop=1.5,
    prob=0.95, expandtomarkers=FALSE, ...)

## S3 method for class 'mapframe'
getQTLIntervals(x, chr = NULL, ci.function = c("lodint",
  "bayesint"), drop = 1.5, prob = 0.95, expandtomarkers = FALSE,
  threshold = NULL, lodcolumn = NULL, qtl.peaks = NULL, ...)

## S3 method for class 'qtl'
getQTLIntervals(x, chr = NULL, ci.function = c("lodint",
  "bayesint"), drop = 1.5, prob = 0.95, expandtomarkers = FALSE,
  qtl.indices = NULL, ...)

## S3 method for class 'scanone'
getQTLIntervals(x, chr = NULL, ci.function = c("lodint",
  "bayesint"), drop = 1.5, prob = 0.95, expandtomarkers = FALSE,
  threshold = NULL, lodcolumn = NULL, qtl.peaks = NULL, ...)

`x`	A `scanone` or `qtl` object.
`chr`	Vector indicating which sequences to consider. If no sequences are specified, QTL intervals are returned for all available sequences.
`ci.function`	Option to indicate which 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.
`...`	Further arguments (see below).
`threshold`	For a `scanone` or equivalent object, this contains a single `numeric` LOD significance threshold, or an object (e.g. `summary.scanoneperm`) containing one such threshold and its associated significance level.
`lodcolumn`	In a `scanone` or equivalent object, this parameter indicates which LOD column to consider. In other objects with LOD-column-associated elements, this parameter indicates which LOD-column-associated element 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.
`qtl.peaks`	Locus `mapframe` indicating the location of the QTL peaks in a `scanone` result. If not specified, these are inferred from the LOD profile of the `scanone` object.
`qtl.indices`	In a `qtl` object, this option indicates the QTLs for which a QTL interval should be returned.

An object of class qtlintervals, which is essentially a list of data.frame objects, each containing three rows of information about the lower QTL interval limit, QTL peak, and upper QTL interval limit, respectively. Returns an empty qtlintervals object if there are no significant QTLs.

Thomas Walsh <tw164@protonmail.com>

Yue Hu

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)

R/qtl manual

Other QTL functions: estPhysicalPositions, getQTLFeatures, getQTLPeaks, plotQTLScanone

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.