Matrix eQTL Update History

• 2014, February 24 — Update. Version 2.1.0
  • Added support for more than 3 ANOVA categories (see modelANOVA).
  • Added option to reduce memory consumption for large gene data sets.
    options(MatrixEQTL.dont.preserve.gene.object)
  • Faster cis-only analysis. Much faster for small cisDist and small slice sizes.
  • File names for the output can now also be connections or NULL.
  • Redesign of QQ-plots.
  • The plot function now follows the R convention and uses ylim instead of ymin parameter.
  • Fixed a bug occurring for genes collinear with covariates.
  • Removed extra space in the output header (for linear models with beta estimates)
  • Sets pvbins are now fixed for QQ-plots. This makes aggregation of results easier.
• 2013, September 3 — Huge update. Version 2.0.0
  • Half of the code and most of the manual/website rewritten.
  • Added effect sizes to the output.
  • Added option to record best p-value for each gene/SNP regardless of p-value threshold.
  • Added option to turn off FDR calculation and write output file in the process, not at the end.
  • Fixed FDR calculation for trans tests (small difference in q-values).
  • Fixed: Gene-SNP pairs are local if the distance between them is less or equal to cisDist (was a strict comparison before).
  • Included toy data set in the package (less than 3kb).
• 2012, August 21 — Minor update. Version 1.6.2.
  • Added rowNamesColumn parameter to SlicedData$LoadFile(...).
  • Added rowSums, rowMeans, colSums, colMeans for SlicedData objects.
  • Removed reference to non-public R function (.C("bincount")) for compatibility with future versions of R.
  • summary(SlicedData) is an S3 method now.
• 2012, May 29 — Another big update (R version only). Version 1.6.1.
  
  • Implemented plot() function for p-value histograms and QQ plots.
  • Improved memory efficiency for 0/1/2/NA genotypes (1 byte per value).
  • Matrix eQTL can now handle datasets with more than 2,147,483,647 values (R limit for vectors/matrices).
  • Files with offset column labels (e.g. created by write.table()) are now read correctly.
  • Location-ignoring analysis saves eQTLs directly without FDR calculation when p-value threshold is too high (the expected output exceeds 1,000,000 rows).
  • Added more information to the object returned by the analysis function (call parameters, gene/SNP names for eQTLs).
  • Added generic methods for SlicedData, including colnames<-, rownames<-, as.matrix. Updated RowReorder, and FindRow methods.
  • Some bugs fixed.
• 2012, May 5 — Added support of SlicedData objects to as.matrix generic. Minor Fixes. Version 1.5.3.
• 2012, Feb 12 — Fixed an incompatibility with R 2.12.0. (It does not have function simplify2array yet.) Version 1.5.2.
• 2012, Feb 12 — Fixed an incompatibility with some versions of R. Version 1.5.1.
• 2012, Feb 5 — MAJOR UPDATE (R version only). Use update.packages() to update the package to version 1.5.0.
  • Added new mode: useModel = modelLINEAR_CROSS to test for SNP-covariate interaction.
  • Added option to plot histogram of p-values for (all/local/distant) tests (including not significant).
  • Greatly improved performance of cis-eQTL analysis, added the option for cis-only analysis.
  • Memory consumption is reduced by 50% when the genotype matrix is integer.
  • Added methods to SlicedData class, including SaveFile, CreateFromMatrix, RowReorder, and FindRow.
  • Added generic methods for SlicedData, including colnames, dim, length, ncol, nrow, rownames, show, and summary.
  • The code is redesigned for easier addition of new models.
  • Some bugs fixed.
• 2011, Dec 9 — Updated R/qtl timing in the table. The previous tests used a suboptimal parameter (method = 'mr' instead of method = 'hk'). My apologies to all R/qtl fans.
• 2011, Oct 6 — Major Update. Use update.packages() to update the package in R.
  • Added FDR calculation.
  • Memory required for ANOVA model is reduced.
  • Added option of separate treatment of cis- (local) and trans- (distant) eQTLs. (Matrix_eQTL_engine_cis.r, R only for now.)
  • The eQTL function does not change the input matrices now (snps, gene, and cvrt).
  • Fixed R code to avoid the ``Design Flaws in R #1 — Reversing Sequences'' .
  • Replaced my implementation of Gram–Schmidt process with a simple call of QR factorization.
  • Replaced !is.finite with is.na.
  • Several minor bugs fixed.
• 2011, Aug 14 — Added a column with the test statistic to the output file (t-statistics show the direction of the effect).
• 2011, Aug 14 — Constant genes and those colinear to the covariates are now removed from the analysis.
• 2011, Aug 14 — Fixed mistreatment of missing values in the R version (is.nan is replaced with !is.finite).
• 2011, Jul 7 — R code is now available as MatrixEQTL package through CRAN.
• 2011, Jul 7 — Improved performance of SlicedData.ResliceCombined in Matlab.
• 2011, Jun 21 — Added support for input files with no row and/or column labels.
• 2011, Jun 19 — Added various bound checks, corrected treatment of pvOutputThreshold = 1.
• 2011, Jun 5 — Added large sample dataset (7zip archive, 1.9mb packed, 1.15gb unpacked).
• 2011, Jun 4 — Fasten creation of ANOVA dummies in R code.
• 2011, Jun 4 — Reduced memory consumption in both implementations.
• 2011, Jun 1 — Due to a performance bug in R, switched from using list to environment for data storage.
• 2011, May 31 — Fixed slow data preprocessing (for large data) in R code.
• 2011, May 30 — Introduced R code for Matrix eQTL.
• 2011, May 26 — Introduced Matlab code for Matrix eQTL.

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By Andrey Shabalin