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https://www.genetics.org/content/genetics/143/2/1013.full.pdf
samples) QTL mapping analyses were done. LOD drop-off support interval: For limited combinations of parameters, confidence intervals were calculated also with the LOD drop-off method. In these cases, a putative QTL wdS fitted at 1-cM intervals, and a support interval was constructedCited by: 658
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207319/
In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location.Cited by: 658
https://www.biostars.org/p/131005/
I would like to get either a Bayes interval or a 1.5 LOD support interval, but the book I am using (A Guide to QTL Mapping with R/qtl) seems to indicate that both these functions assume a single QTL per trait. I would assume that with multiple QTL mapping you get multiple significant peaks and …
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009039
Background Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs) for QTL. Support interval (SI) methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping ...Cited by: 4
https://rqtl.org/rqtltour2.pdf
Interval estimates of QTL location For the blood pressure phenotype, we’ve seen good evidence for QTL on chromosomes 7 and 15. Interval estimates of the location of QTL are commonly obtained via 1.5-LOD support intervals, which may be calculated via the function lodint.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569776/
LOD support intervals are the most commonly used interval estimates for the location of a QTL. A LOD support interval is defined as the interval in which the LOD score is within some value of its maximum. As an illustration, Figure 1A displays the LOD curve for chromosome 4 for the data of S ugiyama et al. ...Cited by: 180
https://www.nature.com/articles/hdy199757
The confidence interval for the map location of quantitative trait loci (QTL) is a very important quantity for geneticists. The one LOD support interval has been proved to be a biased confidence ...Cited by: 21
https://www.genetics.org/content/152/3/1203
Jul 01, 1999 · A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With ...Cited by: 1094
https://rdrr.io/cran/qtl/man/lodint.html
If TRUE, the interval is expanded to the nearest flanking markers. Value An object of class scanone indicating the estimated QTL position and the approximate endpoints for the LOD support interval.
https://www.rdocumentation.org/packages/eqtl/versions/1.1-7/topics/define.peak
The subjective quality of the support interval. A QTL whose support interval can be reached and defined, has more weight than a QTL whose support interval cannot and has been defined by its maximum size (argument m).This quality information corresponds to symbols indicating, how each were defined by the bounds of the QTL support interval.
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