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.

AuthorAndrey Shabalin
Date of publication2015-02-03 06:53:36
MaintainerAndrey Shabalin <ashabalin@vcu.edu>
LicenseLGPL-3
Version2.1.1
http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

View on CRAN

Functions

as.matrix,SlicedData-method Man page
colMeans,SlicedData-method Man page
colnames<-,SlicedData-method Man page
colnames,SlicedData-method Man page
colSums,SlicedData-method Man page
Covariates Man page
dim,SlicedData-method Man page
GE Man page
geneloc Man page
length,SlicedData-method Man page
MatrixEQTL Man page
MatrixEQTL_cis_code Man page
Matrix_eQTL_engine Man page
Matrix_eQTL_main Man page
MatrixEQTL-package Man page
modelANOVA Man page
modelLINEAR Man page
modelLINEAR_CROSS Man page
ncol,SlicedData-method Man page
NCOL,SlicedData-method Man page
nrow,SlicedData-method Man page
NROW,SlicedData-method Man page
plot.MatrixEQTL Man page
rowMeans,SlicedData-method Man page
rownames<-,SlicedData-method Man page
rownames,SlicedData-method Man page
rowSums,SlicedData-method Man page
show,SlicedData-method Man page
SlicedData Man page
SlicedData-class Man page
SlicedData-class Man page
[[<-,SlicedData-method Man page
[[,SlicedData-method Man page
SNP Man page
snpsloc Man page
summary.SlicedData Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.