FlexLMM: a Nextflow linear mixed model framework for GWAS
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arXiv
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| Autores principales: | , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866916420724457472 |
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| author | Pierotti, Saul Fitzgerald, Tomas Birney, Ewan |
| author_facet | Pierotti, Saul Fitzgerald, Tomas Birney, Ewan |
| contents | Summary: Linear mixed models are a commonly used statistical approach in genome-wide association studies when population structure is present. However, naive permutations to empirically estimate the null distribution of a statistic of interest are not appropriate in the presence of population structure, because the samples are not exchangeable with each other. For this reason we developed FlexLMM, a Nextflow pipeline that runs linear mixed models while allowing for flexibility in the definition of the exact statistical model to be used. FlexLMM can also be used to set a significance threshold via permutations, thanks to a two-step process where the population structure is first regressed out, and only then are the permutations performed. We envision this pipeline will be particularly useful for researchers working on multi-parental crosses among inbred lines of model organisms or farm animals and plants.
Availability and implementation: The source code and documentation for the FlexLMM is available at https://github.com/birneylab/flexlmm. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2410_01533 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | FlexLMM: a Nextflow linear mixed model framework for GWAS Pierotti, Saul Fitzgerald, Tomas Birney, Ewan Genomics Summary: Linear mixed models are a commonly used statistical approach in genome-wide association studies when population structure is present. However, naive permutations to empirically estimate the null distribution of a statistic of interest are not appropriate in the presence of population structure, because the samples are not exchangeable with each other. For this reason we developed FlexLMM, a Nextflow pipeline that runs linear mixed models while allowing for flexibility in the definition of the exact statistical model to be used. FlexLMM can also be used to set a significance threshold via permutations, thanks to a two-step process where the population structure is first regressed out, and only then are the permutations performed. We envision this pipeline will be particularly useful for researchers working on multi-parental crosses among inbred lines of model organisms or farm animals and plants. Availability and implementation: The source code and documentation for the FlexLMM is available at https://github.com/birneylab/flexlmm. |
| title | FlexLMM: a Nextflow linear mixed model framework for GWAS |
| topic | Genomics |
| url | https://arxiv.org/abs/2410.01533 |