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MatrixEQTL (version 2.1.0)

MatrixEQTL: Ultra fast eQTL analysis via large matrix operations

Description

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.

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Version

Install

install.packages('MatrixEQTL')

Monthly Downloads

574

Version

2.1.0

License

LGPL-3

Maintainer

Andrey Shabalin

Last Published

February 25th, 2014

Functions in MatrixEQTL (2.1.0)

geneloc

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

Artificial data for Matrix eQTL sample code: Gene expression.
SlicedData-class

Class SlicedData for storing large matrices
modelLINEAR

Constant for Matrix_eQTL_engine.
MatrixEQTL-package

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
SNP

Artificial data for Matrix eQTL sample code: Genotype.
plot.MatrixEQTL

Plot histogram or QQ-plot of all p-values
modelANOVA

Constant for Matrix_eQTL_engine.
modelLINEAR_CROSS

Constant for Matrix_eQTL_engine.
Covariates

Artificial data for Matrix eQTL sample code: Covariates.
Matrix_eQTL_main

Main function for fast eQTL analysis in MatrixEQTL package
MatrixEQTL_cis_code

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

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