du.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • chicago-author-date
  • chicago-note-bibliography
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
A Monte Carlo Full Likelihood Approach in Variance Component Quantitative Trait Loci Analysis
Dalarna University, School of Technology and Business Studies, Statistics.ORCID iD: 0000-0003-4390-1979
2009 (English)In: 13th QTLMAS Workshop, Wageningen, The Netherlands, 2009Conference paper, Published paper (Other academic)
Abstract [en]

The identity-by-descent (IBD) matrix is the core of the variance component QTL model. The true IBD matrix comes from a distribution of IBD matrices given the marker information, but its expectation is normally used in QTL analysis. This gives incorrect likelihood values since the extra uncertainty in estimating the IBD matrix is not included. Previous studies have concentrated on small pedigrees where the correct likelihood can be derived. For large pedigrees this approach is not feasible. We therefore developed a Monte Carlo method for calculating the likelihood in- corporating the uncertainty of the estimated IBD matrix. The aim of this study is to implement the Monte Carlo Full Likelihood (MCFL) algorithm and to compare the true likelihood with the like- lihood based on the expected IBD matrix for large pedigrees. Our simulation results show that the likelihood based on the expected IBD matrix approximates the true likelihood well and may there- fore justify the use of the expected IBD matrix in empirical QTL analysis. Our MCFL method can actually be computationally more efficient than the expectation method for large pedigrees with a small founder generation, because the rank of the true IBD matrix is much lower than the rank of the expected IBD matrix, especially when the genetic markers are highly informative. Using the IBD matrices produced in our MCFL method we may also simplify the modeling of epistasis for linked QTL.

Place, publisher, year, edition, pages
Wageningen, The Netherlands, 2009.
Identifiers
URN: urn:nbn:se:du-4844OAI: oai:dalea.du.se:4844DiVA, id: diva2:522143
Conference
13th QTLMAS Workshop , Wageningen, The Netherlands, 20-21 april, 2009
Available from: 2010-06-18 Created: 2010-06-18 Last updated: 2015-06-16Bibliographically approved

Open Access in DiVA

No full text in DiVA

Authority records BETA

Shen, Xia

Search in DiVA

By author/editor
Shen, Xia
By organisation
Statistics

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 511 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • chicago-author-date
  • chicago-note-bibliography
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf