NEWS

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RnBeads 2.19.0

• Fixed issue with logical having a length greater than 1

RnBeads 2.17.1

• Temporarily removed the GLAD dependency and CNV functionality

RnBeads 2.17.0

• Fixed bug in differential variability analysis

RnBeads 2.15.1

• Added custom reimplementations of dye-bias and background correction methods from SeSaMe

RnBeads 2.13.2

• Removed support for RefFreeEWAS, since the package is not supported anymore

RnBeads 2.13.0

• Compatibility fixes with SeSaMe by zwdzwd
• Minor bugfixes

RnBeads 2.11.0

• Bugfixes in MMBC support

RnBeads 2.9.4

• Added initial version of the Mouse Methylation Bead Chip support
• Native implementations of basic dye-bias and background correction methods (methylumi dependency removed)

RnBeads 2.9.3

• Changed some of the default options values
• Some bugfixes

RnBeads 2.9.2

• Implemented function rnb.execute.pOOBAH. Thanks to Nathan Steenbuck.
• Update of contact information in DESCRIPTION

RnBeads 2.9.1

• Improved function intensities.by.color. Thanks to Nathan Steenbuck.

RnBeads 2.7.1

• Added conversion from RnBeadRawSet to RGChannelSet

RnBeads 2.3.3

• Fixed non ASCII column names in age prediction and immune estimation

RnBeads 2.3.2

• Added stratification plots for inferred covariates in different sample groups

RnBeads 2.1.3

• Implemented methylation based segmentation by the MethylSeekR approach. Thanks to Abdulrahman Salhab for providing code for the integration.
• Wrapper for load.rnb.set

RnBeads 2.1.2

• Fix in as.RnBeadRawSet
• Added new paper to CITATION

RnBeads 2.1.1

• Added support for SLURM compute cluster architecture

RnBeads 1.99.0

• RnBeadsDJ: updated documentation and tooltips
• deactivated intersample plots (exploratory module) as default option for BS-seq data
• Roxygen documentation updates
• Extended methods descriptions in reports (imputation, filtering, differential, ...)
• Miscellaneous bugfixes and performance improvements in RnBeadsDJ, imputation, ...

RnBeads 1.13.3

• added CNV estimation using the GLAD package to QC module
• some bugfixes
• changed 'gender' to 'sex', affected functions and options are 'rnb.execute.gender.prediction' and 'import.gender.prediction'

RnBeads 1.13.2

• added qvalue to suggested packages

RnBeads 1.13.1

• Updated LOLA DB download links

RnBeads 1.11.9

• Bugfixes and improvements in gender prediction, GEO import, differential variability, installation and others

RnBeads 1.11.8

• Fixes for bioconductor warnings (combine, etc.)
• docoupled missing value imputation from differential methylation

RnBeads 1.11.7

• enhanced cross-platform combination methods
• improved installation routines
• enhanced plots in exploratory analysis module
• better LOLA annotation
• improved performance of missing value imputation
• documentation updates
• several minor bugfixes

RnBeads 1.11.6

• Improved combining methods for RnBSet objects of different data types
• Interpretation of sample mean methylation levels and other statistics
• Improved plots in exploratory analysis module
• Improved missing value imputation
• Several minor bugfixes

RnBeads 1.11.5

• bugfixes (loading, imputation)

RnBeads 1.11.4

• Introducing RnBeadsDJ, a shiny-based interface for running RnBeads analyses and modules (run with rnb.run.dj())
• Added implementation of the LUMP algorithm for immune cell content estimation
• The default normalization method was changed to "wm.dasen"
• Background normalization is now disabled per default.
• Option backwards compatibility
• bugfixes (LOLA dependencies, 1-sample differential variability, QC visualization, ...)

RnBeads 1.11.2

• Fixed a bug concerning failed trackhub exports on Windows

RnBeads 1.9.4

• You can now retrieve custom region sets from the RnBeads resource using the rnb.load.annotation.from.db function
• improved import from GEO
• bigff disk dump is now the default option for dealing with disk-based big matrices
• Several bugfixes and performance improvements in Greedycut, normalization, Bisulfite data loading and others
• Added differential variability analysis in addition to differential methylation

RnBeads 1.9.3

• LOLA support for differentially methylated regions
• various LOLA utitility functions
• What used to be the "differential.enrichment" option is now called "differential.enrichment.go" to reflect the distinction between GO and LOLA enrichment analyses
• Missing methylation data can now be imputed (using mean, random or nearest-neighbor imputation)
• Gender prediction now supports sequencing and EPIC data
• Added a function for combining two array-based datasets from (potentially) different platforms.
• Several bugfixes and performance improvements

RnBeads 1.7.5

• Several minor bugfixes and performance improvements
• added a vignette section on working with RnBSet objects

RnBeads 1.7.4

• Several minor bugfixes and performance improvements
• Vignette installation instructions updated
• Reduce warnings in R CMD check

RnBeads 1.7.3

• Age predictor (MethylAger) updates and documentation
• Support for external tools bedToBigBed and bedGraphToBigWig
• Minor bugfixes

RnBeads 1.7.2

• Added genetic purity estimation based on SNP probes (option qc.snp.purity, microarrays only)

RnBeads 1.7.1

• Added support for the ENmix.oob background subtraction method
• Several improvements in age prediction module
• Added conversion from minfi raw dataset to RnBeadRawSet
• Several minor bug fixes

RnBeads 1.5.1

• Reference-based cell type composition estimation now uses the 50,000 most variable sites by default.
• Minor bug fixes

RnBeads 1.3.8

• Added age prediction from 450K and bisulfite data to inference module

RnBeads 1.3.7

• Subsampling for reporting and plotting methylation values distributions in filtering report to reduce memory footprint.

RnBeads 1.3.6

• Support for Illumina EPIC array and related bugfixes
• Added a section on whitelist and blacklist in the Preprocessing module

RnBeads 1.3.5

• Fixes with ggplot in 450K array QC plotting
• Added an option 'differential.report.sites' to decrease runtime by skipping the differential site methylation section in the report

RnBeads 1.3.4

• Added support for Illumina EPIC array

RnBeads 1.3.3

• Added 'smooth.profile' parameter to rnb.plot.locus.profile function

RnBeads 1.3.2

• Performance and memory improvements during loading, qc and preprocessing of large bisulfite-derived RnBSets
• Added optional arguments to meth() and covg() allowing for partial retrieval of methylation and coverage information from RnBSets. Particularly makes sense for large, disk-based datasets.
• Added option "disk.dump.bigff.finalizer" for setting the finalizer for temporary BigFfMat objects

RnBeads 1.3.1

• Added "remove.regions" function for RnBSet class
• summarize.regions now summarizes for each sample individually in order to reduce memory consumption for large WGBS datasets
• import.skip.object.check option for keeping the memory profile low while loading huge datasets
• NA sites (filtering.missing.value.quantile) are now removed even if they were previously masked (filtering.low.coverage.masking)
• Added "nsites" method for quickly extracting the number of sites for large RnBSet objects without having to retrieve the full methylation matrix
• Added "hasCovg" method for quickly determining whether coverage information is present in large RnBSet objects without having to retrieve the full coverage matrix

RnBeads 1.1.9

• Filtering report fix when no normalization is conducted
• Bugfixes for combine(RnBSet, RnBSet) and BigFf matrices

RnBeads 1.1.8

• Corrected coverage statistics in sample summary table: Sites with NA methylation values are no longer considered in the coverage statistics (makes a difference if some coverage threshold is applied)
• Improved method for gender prediction. Predicted genders are also included in the exported annotation table

RnBeads 1.1.7

• Improvements to mergeSamples function for RnBiseqSets
• Some more memory clean-up

RnBeads 1.1.6

• Differential methylation based on region level only is now supported
• Minor updates to the differential methylation report generation
• Performance improvements and minor bugfixes for using disk.dump.bigff
• Performance improvements (more memory clean-up)

RnBeads 1.1.5

• New option: disk.dump.bigff for using a wrapper class of the ff package to avoid their INT_MAX issue

RnBeads 1.1.4

• Fixes in parallel environment setup from bioconcuctor

RnBeads 1.1.3

• Some fixes in data loading
• Fixes in parallel environment setup

RnBeads 1.1.2

• New annotation package format
• Support for filtering out cross-reactive probes in Infinium 450k dataset
• Improved logging on a Mac

RnBeads 1.0.0

• Bioconductor release

RnBeads 0.99.23

• Incorporated some bioconductor check related improvements

RnBeads 0.99.22

• Incorporated bioconductor requirements for parallel processing. "parallel.disable" is now "parallel.teardown"

RnBeads 0.99.20

• RnBeads no longer suggests IlluminaHumanMethylation450k.db.

RnBeads 0.99.19

• Fixed a bug in the computation of surrogate variables (SVA) that did not take into account other adjustment variables in the model (compared to the null model)
• Updated locus profiles to work with the latest version of Gviz
• Differential methylation reports now contain information on group sizes
• Included plots of number of sites vs coverage percentiles for each sample in the dataset (rnb.plot.num.sites.covg)
• Bisulfite-seq QC reports now contain an additional section with summary statistics and plots when the coverage histogram plots are enabled

RnBeads 0.99.18

• Implementation of class constructors (the S4 constructors are not available anymore)
• Analyses can now be started from an RnBSet which is stored on the hard drive (using save.rnb.set) via the rnb.set.dir data type
• New IDAT loading routine, based on the illuminaio package
• Multiple fixes in wrappers for wateRmelon normalization methods
• Fixed the RefFreeEWAS wrapper
• Updated the Houseman, 2012 reference-based method implementation
• RnBSets now know the version with which they were created
• Various other bugfixes and improvements to reports and documentation

RnBeads 0.99.17

• Consistency issues with Bioconductor 3.0 fixed
• Fixed a bug relating to no coverage masking being conducted for sequencing data
• Various other bugfixes

RnBeads 0.99.16

• Enhanced XML-based analysis though the tag preanalysis.script
• Optimized loading of the sequencing data sets
• Enhanced region profiles plots. Added region site distribution plots
• Locus profiles can now be generated in the exploratory report for regions specified in custom bed files and for genes listed as gene symbols
• Improved cell type heterogeneity inference (no cell types excluded anymore)
• Added more support for paired differential methylation with limma
• Some functions were renamed: merge.samples->mergeSamples, add.pheno->addPheno, add.region.subsegments->addRegionSubsegments, and all functions operating on Report
• Added helper classes for submitting RnBeads to a scientific compute cluster. Current implementation includes Sun Grid Engine
• The default pipeline now uses ff functionality and saves intermediate objects into the report directory
• Minor bugfixes

RnBeads 0.99.15

• Restructuring of the pipeline modules: ** the loading module has been renamed to import ** the prefiltering,normalization and postfiltering modules have been summarized in a new module: preprocessing ** the batch and profiles modules have been summarized in a new module for exploratory analysis ** the export module has been renamed to tracks and tables ** corresponding option names have been changed ** see the overview figure on the website or the vignette for a quick overview on the new module structure
• Multiple RnBSets can now be concatenated with the add() function
• Multiple samples in an RnBSet can be merged using the merge.samples() function
• Gender prediction can be performed on Infinium 450k datasets
• Minor updates on covariate adjustment
• Updates on tissue heterogeneity estimation
• Calling differentially methylated sites with RefFreeEWAS now supports paired design
• Multiple minor bugfixes and performance improvements
• Vignette and documentation updates

RnBeads 0.99.13

• Added new module on annotation inference
• Added correction for cell type heterogeneity
• Added SVA functionality
• Minor bugfixes
• Updates to the vignette and other documentation

RnBeads 0.99.12

• Support Bismark coverage file loading
• Enhanced documentation and logging of loading steps
• Minor bugfixes
• Updates to the vignette and other documentation RnBeads 0.99.11
• Accommodate data packages for individual genomes
• Performance: disk space usage when using disk dumping, options for subsetting sites when computing distance matrices for clustering, PCA and MDS
• Region subsegmentation
• The default method for differential methylation p-values is limma

RnBeads 0.99.10

• Performance improvements
• Option to keep big matrices on the hard drive rather than main memory
• Restructuring of the filtering modules. Parts of the filtering steps are executed before normalization others afterwards
• Improvements in normalization: more methods supported
• Cosmetic changes to some of the plots

RnBeads 0.99.9

• Bugfixes in paired analysis
• Usability of bisulfite sequencing

RnBeads 0.99.8

• New normalization methods integrated
• Improved arguments to rnb.run.analysis
• Improved parsing of the sample annotation table
• Paired analysis (testing stage)
• Webservice installed
• Multiple bugfixes

RnBeads 0.99.7

• Support for background subtraction and BMIQ normalization of Infinium 450k data
• Support for differential methylation analysis on all pairs of sample groups

RnBeads 0.99.6

• Locus Profiles
• Support for parallel computing

RnBeads 0.99.0

• Many additional features including bisulfite sequencing mode, the mouse genome, data export, ...

RnBeads 0.5.0

• Initial release of RnBeads containing six modules - loading and normalization, quality control, filtering, batch effects, methylation profiles and differential methylation.