Package: MatrixEQTL 2.3
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>.
Authors:
MatrixEQTL_2.3.tar.gz
MatrixEQTL_2.3.zip(r-4.5)MatrixEQTL_2.3.zip(r-4.4)MatrixEQTL_2.3.zip(r-4.3)
MatrixEQTL_2.3.tgz(r-4.4-any)MatrixEQTL_2.3.tgz(r-4.3-any)
MatrixEQTL_2.3.tar.gz(r-4.5-noble)MatrixEQTL_2.3.tar.gz(r-4.4-noble)
MatrixEQTL_2.3.tgz(r-4.4-emscripten)MatrixEQTL_2.3.tgz(r-4.3-emscripten)
MatrixEQTL.pdf |MatrixEQTL.html✨
MatrixEQTL/json (API)
| # Install 'MatrixEQTL' in R: |
| install.packages('MatrixEQTL', repos = c('https://andreyshabalin.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/andreyshabalin/matrixeqtl/issues
- Covariates - Artificial data for Matrix eQTL sample code: Covariates.
- GE - Artificial data for Matrix eQTL sample code: Gene expression.
- SNP - Artificial data for Matrix eQTL sample code: Genotype.
- geneloc - Artificial data for Matrix eQTL sample code: Gene location file.
- snpsloc - Artificial data for Matrix eQTL sample code: SNP location file.
Last updated 12 months agofrom:f88f97e07a. Checks:OK: 1 ERROR: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 21 2024 |
| R-4.5-win | ERROR | Aug 21 2024 |
| R-4.5-linux | ERROR | Aug 21 2024 |
| R-4.4-win | ERROR | Aug 21 2024 |
| R-4.4-mac | ERROR | Aug 21 2024 |
| R-4.3-win | ERROR | Aug 21 2024 |
| R-4.3-mac | ERROR | Aug 21 2024 |
Exports:as.matrixcolMeanscolnamescolnames<-colSumsMatrix_eQTL_engineMatrix_eQTL_mainmodelANOVAmodelLINEARmodelLINEAR_CROSSncolNCOLnrowNROWrowMeansrownamesrownames<-rowSumsSlicedData
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations | MatrixEQTL-package MatrixEQTL |
| Artificial data for Matrix eQTL sample code: Covariates. | Covariates |
| Artificial data for Matrix eQTL sample code: Gene expression. | GE |
| Artificial data for Matrix eQTL sample code: Gene location file. | geneloc |
| Main function for fast eQTL analysis in MatrixEQTL package | Matrix_eQTL_engine Matrix_eQTL_main |
| Sample code for cis/trans-eQTL analysis with Matrix eQTL | MatrixEQTL_cis_code |
| Constant for 'Matrix_eQTL_engine'. | modelANOVA |
| Constant for 'Matrix_eQTL_engine'. | modelLINEAR |
| Constant for 'Matrix_eQTL_engine'. | modelLINEAR_CROSS |
| Plot histogram or QQ-plot of all p-values | plot.MatrixEQTL |
| Class 'SlicedData' for storing large matrices | as.matrix,SlicedData-method colMeans,SlicedData-method colnames,SlicedData-method colnames<-,SlicedData-method colSums,SlicedData-method dim,SlicedData-method length,SlicedData-method NCOL,SlicedData-method ncol,SlicedData-method NROW,SlicedData-method nrow,SlicedData-method rowMeans,SlicedData-method rownames,SlicedData-method rownames<-,SlicedData-method rowSums,SlicedData-method show,SlicedData-method SlicedData SlicedData-class summary.SlicedData [[,SlicedData-method [[<-,SlicedData-method |
| Artificial data for Matrix eQTL sample code: Genotype. | SNP |
| Artificial data for Matrix eQTL sample code: SNP location file. | snpsloc |
