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.

Author
Andrey Shabalin
Date of publication
2015-02-03 06:53:36
Maintainer
Andrey Shabalin <ashabalin@vcu.edu>
License
LGPL-3
Version
2.1.1
URLs

View on CRAN

Man pages

Covariates
Artificial data for Matrix eQTL sample code: Covariates.
GE
Artificial data for Matrix eQTL sample code: Gene expression.
geneloc
Artificial data for Matrix eQTL sample code: Gene location...
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
MatrixEQTL-package
Matrix eQTL: Ultra fast eQTL analysis via large matrix...
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
SlicedData-class
Class 'SlicedData' for storing large matrices
SNP
Artificial data for Matrix eQTL sample code: Genotype.
snpsloc
Artificial data for Matrix eQTL sample code: SNP location...

Files in this package

MatrixEQTL
MatrixEQTL/inst
MatrixEQTL/inst/CITATION
MatrixEQTL/NAMESPACE
MatrixEQTL/demo
MatrixEQTL/demo/e.interaction.r
MatrixEQTL/demo/d.ANOVA5.r
MatrixEQTL/demo/c.weights.r
MatrixEQTL/demo/sample.cis.r
MatrixEQTL/demo/sample.all.r
MatrixEQTL/demo/d.ANOVA.r
MatrixEQTL/demo/00Index
MatrixEQTL/demo/a.nocvrt.r
MatrixEQTL/demo/q.qqplot.r
MatrixEQTL/demo/b.cvrt.r
MatrixEQTL/demo/p.hist.r
MatrixEQTL/data
MatrixEQTL/data/GE.txt
MatrixEQTL/data/snpsloc.txt
MatrixEQTL/data/SNP.txt
MatrixEQTL/data/Covariates.txt
MatrixEQTL/data/geneloc.txt
MatrixEQTL/R
MatrixEQTL/R/Matrix_eQTL_engine.R
MatrixEQTL/MD5
MatrixEQTL/DESCRIPTION
MatrixEQTL/man
MatrixEQTL/man/Covariates.Rd
MatrixEQTL/man/figures
MatrixEQTL/man/figures/QQplot.png
MatrixEQTL/man/figures/histogram.png
MatrixEQTL/man/plot.MatrixEQTL.Rd
MatrixEQTL/man/modelLINEAR.Rd
MatrixEQTL/man/MatrixEQTL_cis_code.Rd
MatrixEQTL/man/geneloc.Rd
MatrixEQTL/man/Matrix_eQTL_main.Rd
MatrixEQTL/man/MatrixEQTL-package.Rd
MatrixEQTL/man/SlicedData-class.Rd
MatrixEQTL/man/modelANOVA.Rd
MatrixEQTL/man/SNP.Rd
MatrixEQTL/man/modelLINEAR_CROSS.Rd
MatrixEQTL/man/GE.Rd
MatrixEQTL/man/snpsloc.Rd