RAMEN 2.0.0 #1
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RAMEN 2.0.0 #1
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…1, EPICv2 or 450k), without providing the manifest
…an option of using the ultrastable probes to determine the variability threshold
…s long as there are more than 100 ultrastable probes in their data set.
…upports users providing array data frames
…th the direct output of selectVariables
…n-unique column names
…utput now is a data frame for VML, and both VMRs and sVMPs are in a single data frame.
…ould make the function give an undesired output when methylation_data was a matrix.
…notation packages.
…n crash in the middle of the process.
… first ones to be checked
Merge branch 'master' into vmr_var_threshold # Conflicts: # R/findVMRs.R # README.Rmd # README.md # vignettes/RAMEN.Rmd
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RAMEN 2.0.0
In this version, we have made an important change in RAMEN terminology across all the code and documentation to more accurately reflect the biological concepts represented by the data. The term "Variably Methylated Regions (VMR)" used in RAMEN v1 has been replaced by "Variably Methylated Loci (VML)" in RAMEN v2, as not all VML are composed of 2 or more highly variable probes. VML are further composed of Variably Methylated Regions (previously named "canonical VMR" in RAMEN v1) and sparse Variably Methylated Probes (sVMPs; previously named "non-canonical VMR" in RAMENv1). To be clear, there are no changes in how these VML are identified, we only changed how we label these categories.
: Terminology update
To reflect the terminology change, the following functions had a name change:
findVML()(previously namedfindVMRs()in RAMEN v1) andsummarizeVML()(previously namedsummarizeVMRs()in RAMEN v1).findVML():Output: list does not separate VMRs and sVMPs into two different list elements anymore. Now, a single element ("VML") is returned in the output list, which contains both VMRs and sVMPs, labelled accordingly under the type column; this VML element is now a data frame, and not a Genomic Ranges object to facilitate data wrangling and plotting. The function now automatically indexes the VML.
The user does not need to provide the array manifest anymore if working with the Illumina 450k, EPICv1 or EPICv2 array. The
array_manifestargument accepts now "IlluminaHumanMethylation450k", "IlluminaHumanMethylationEPICv1" and "IlluminaHumanMethylationEPICv2".There is a new method to identify VML using ultrastable probes (probes which DNA methylation is known to be stable independently of tissue and developmental stage) to discriminate Highly Variable Probes, which are then grouped into VML. This method is the default one now. For more information please see the
findVML()documentation and the package vignette. The previously default method to identify Highly Variable Probes (top 10% of probes with the highest variance in the data set) is still available using the argumentvar_distribution = "all".nullDistGE(): Prints messages to keep track of the progress. Fixed a bug that made doFuture parallelization strategies crash.All functions have examples in the documentation.
Added tests to reach a code coverage of >90% in all functions.
Improved error catches to make functions stop early when the inputs are not in the right format. Fixed various bugs throughout the code (no user.
Added news, citation and contributing files to the repository.
Citation info is provided when loading the package.
The package repository has now informative badges and Continuous Integration checks.