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MatrixEQTL

Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations

Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.

Functions (13)

Covariates

Artificial data for Matrix eQTL sample code: Covariates.

GE

Artificial data for Matrix eQTL sample code: Gene expression.

MatrixEQTL-package

Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations

MatrixEQTL_cis_code

Sample code for cis/trans-eQTL analysis with Matrix eQTL

Matrix_eQTL_main

Main function for fast eQTL analysis in MatrixEQTL package

SNP

Artificial data for Matrix eQTL sample code: Genotype.

SlicedData-class

Class SlicedData for storing large matrices

geneloc

Artificial data for Matrix eQTL sample code: Gene location file.

modelANOVA

Constant for Matrix_eQTL_engine.

modelLINEAR

Constant for Matrix_eQTL_engine.

modelLINEAR_CROSS

Constant for Matrix_eQTL_engine.

plot.MatrixEQTL

Plot histogram or QQ-plot of all p-values

snpsloc

Artificial data for Matrix eQTL sample code: SNP location file.

MatrixEQTL

Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations

v2.3
LGPL-3
Authors
Andrey A Shabalin [aut, cre] (<https://orcid.org/0000-0003-0309-6821>)
Initial release
2019-12-04

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