Matrix eQTL: ultra fast eQTL analysis via large matrix operations
نویسندگان
چکیده
منابع مشابه
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
MOTIVATION Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of transcript-SNP (single-nucleotide polymorphism) pair. The heavy computational burden makes eQTL analysis less popular and sometimes forces analysts to re...
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MOTIVATION Gene expression Quantitative Trait Locus (eQTL) mapping measures the association between transcript expression and genotype in order to find genomic locations likely to regulate transcript expression. The availability of both gene expression and high-density genotype data has improved our ability to perform eQTL mapping in inbred mouse and other homozygous populations. However, exist...
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This vignette describes eQTL mapping, visualization and other analysis tools in R/eMap package. To improve efficiency, we implemented the computational intensive parts of our algorithms by C using GSL library (http://www.gnu.org/software/gsl/). Therefore in order to install this R package, GSL library need to be installed. Users may need to change the Makevars file in src folder to provide the ...
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The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specific...
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Genetic loci that affect mRNA expression levels of other genes are referred to as expression quantitative trait loci (eQTL). Discovering eQTLs by combining gene expression data with genetic marker data is an important means to understand gene regulation and to study disease mechanisms. EQTL mapping has been studied in many species, e.g., yeast [1, 2], eucalyptus [3], mice [4–6], rats [7], and h...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2012
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bts163