eQTL Analysis by Linear Model
نویسنده
چکیده
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 correct location for hearder file and library file of GSL.
منابع مشابه
Robust Linear Models for Cis-eQTL Analysis
Expression Quantitative Trait Loci (eQTL) analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data gener...
متن کاملHEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors
MOTIVATION Identification of expression Quantitative Trait Loci (eQTL), the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis. METHODS We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual a...
متن کاملMatrix 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...
متن کاملAn Information-Theoretic Machine Learning Approach to Expression QTL Analysis
Expression Quantitative Trait Locus (eQTL) analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL), and on other chromosomes (trans-eQTL). Many traditional eQTL methods are based on a linear r...
متن کاملAn independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impac...
متن کامل