MatrixEQTL: Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
Version 2.1.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorAndrey Shabalin
Date of publication2015-02-03 06:53:36
MaintainerAndrey Shabalin <ashabalin@vcu.edu>
LicenseLGPL-3
Version2.1.1
URL http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MatrixEQTL")

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...

Functions

Covariates Man page
GE Man page
MatrixEQTL Man page
MatrixEQTL-package Man page
MatrixEQTL_cis_code Man page
Matrix_eQTL_engine Man page Source code
Matrix_eQTL_main Man page Source code
NCOL,SlicedData-method Man page
NROW,SlicedData-method Man page
SNP Man page
SNP_process_split_for_ANOVA Source code
SetNanRowMean Source code
SlicedData Man page
SlicedData-class Man page Man page
[[,SlicedData-method Man page
[[<-,SlicedData-method Man page
as.matrix,SlicedData-method Man page
colMeans,SlicedData-method Man page
colSums,SlicedData-method Man page
colnames,SlicedData-method Man page
colnames<-,SlicedData-method Man page
dim,SlicedData-method Man page
geneloc Man page
histme Source code
length,SlicedData-method Man page
modelANOVA Man page
modelLINEAR Man page
modelLINEAR_CROSS Man page
my.pmax Source code
my.pmin Source code
ncol,SlicedData-method Man page
nrow,SlicedData-method Man page
plot.MatrixEQTL Man page Source code
pv.nz Source code
qqme Source code
rowMeans,SlicedData-method Man page
rowSums,SlicedData-method Man page
rownames,SlicedData-method Man page
rownames<-,SlicedData-method Man page
seq Source code
show,SlicedData-method Man page
snpsloc Man page
summary.SlicedData Man page Source code

Files

inst
inst/CITATION
NAMESPACE
demo
demo/e.interaction.r
demo/d.ANOVA5.r
demo/c.weights.r
demo/sample.cis.r
demo/sample.all.r
demo/d.ANOVA.r
demo/00Index
demo/a.nocvrt.r
demo/q.qqplot.r
demo/b.cvrt.r
demo/p.hist.r
data
data/GE.txt
data/snpsloc.txt
data/SNP.txt
data/Covariates.txt
data/geneloc.txt
R
R/Matrix_eQTL_engine.R
MD5
DESCRIPTION
man
man/Covariates.Rd
man/figures
man/figures/QQplot.png
man/figures/histogram.png
man/plot.MatrixEQTL.Rd
man/modelLINEAR.Rd
man/MatrixEQTL_cis_code.Rd
man/geneloc.Rd
man/Matrix_eQTL_main.Rd
man/MatrixEQTL-package.Rd
man/SlicedData-class.Rd
man/modelANOVA.Rd
man/SNP.Rd
man/modelLINEAR_CROSS.Rd
man/GE.Rd
man/snpsloc.Rd
MatrixEQTL documentation built on May 19, 2017, 2:06 p.m.