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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
06/12/2011 |
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Data da última atualização: |
24/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
HIGA, R.; BARRICHELLO, F.; NICIURA, S.; MEIRELLES, S.; REGITANO, L. |
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Afiliação: |
ROBERTO HIROSHI HIGA, CNPTIA; FABIANA BARRICHELLO, UFSCar; SIMONE CRISTINA MEO NICIURA, CPPSE; SARAH MEIRELLES, UFLA; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
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Título: |
An R script for quality control in genome-wide association studies. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês |
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Notas: |
X-MEETING 2011. |
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Conteúdo: |
Recent advances in massive genotyping technology based on SNP (Single Nucleotide Polymorphisms) markers are pushing animal breeding research into a new era where the entire genome is screened in the search for genes which affect traits of economic interest, called genome wide association studies (GWAS). The first step in setting up a GWAS is to perform a quality control analysis (QC) on the genotyped data in order to filter out samples and SNPs not satisfying a previously defined set of criteria [1]. The most common criteria include sample and SNP call rate, minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE). It is also recommended to analyze the heterozygosity and the presence of population structure and outlier samples. However, a different set of criteria and thresholds may be more appropriate for different datasets. We wrote an R script [2] which implements a number of QC criteria, making them available as functions and allowing users to use those QC criteria which are more appropriate to their dataset. In this work, we describe a set of functions implemented in our R script and illustrate its use in a GWAS of cattle meat quality in a Canchim cattle breed population. |
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Palavras-Chave: |
Marcadores SNP; Polimorfismo de nucleotídeo único. |
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Thesagro: |
Gado de Corte; Genoma. |
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Thesaurus Nal: |
Cattle; Genome; Single nucleotide polymorphism. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/49423/1/Rscript-.pdf
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Marc: |
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100 1 $aHIGA, R.
245 $aAn R script for quality control in genome-wide association studies.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional$c2011
300 $aNão paginado.
500 $aX-MEETING 2011.
520 $aRecent advances in massive genotyping technology based on SNP (Single Nucleotide Polymorphisms) markers are pushing animal breeding research into a new era where the entire genome is screened in the search for genes which affect traits of economic interest, called genome wide association studies (GWAS). The first step in setting up a GWAS is to perform a quality control analysis (QC) on the genotyped data in order to filter out samples and SNPs not satisfying a previously defined set of criteria [1]. The most common criteria include sample and SNP call rate, minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE). It is also recommended to analyze the heterozygosity and the presence of population structure and outlier samples. However, a different set of criteria and thresholds may be more appropriate for different datasets. We wrote an R script [2] which implements a number of QC criteria, making them available as functions and allowing users to use those QC criteria which are more appropriate to their dataset. In this work, we describe a set of functions implemented in our R script and illustrate its use in a GWAS of cattle meat quality in a Canchim cattle breed population.
650 $aCattle
650 $aGenome
650 $aSingle nucleotide polymorphism
650 $aGado de Corte
650 $aGenoma
653 $aMarcadores SNP
653 $aPolimorfismo de nucleotídeo único
700 1 $aBARRICHELLO, F.
700 1 $aNICIURA, S.
700 1 $aMEIRELLES, S.
700 1 $aREGITANO, L.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| 1. |  | HIGA, R.; BARRICHELLO, F.; NICIURA, S.; MEIRELLES, S.; REGITANO, L. An R script for quality control in genome-wide association studies. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011. Não paginado. X-MEETING 2011.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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