NEWS.md

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

[ 2.1.2 ]

• New default value for argument out.dir of RunHdxParallel and early error checking on creating / writing to out.dir.

[ 2.1.1 ]

• No changes from 2.1.0.3.

[ 2.1.0.3 ]

• Documentation correction for downsample_spectra and typos.

[ 2.1.0.2 ]

• Deprecated argument thres in downsample and downsample_spectra and replaced it with downsample_threshold.
• Minor documentation updates.

[ 2.1.0.1]

• Added function show_downsample_curves.

[ 2.1.0 ]

• Replaced mSigAct with mSigTools for writing and plotting exposure.
• Updated required branch for hdpx.

[ 2.0.1.0010 ]

• Added downsampling capability.

[ 2.0.1.0009 ]

• 2022 06 24 Replaced hc.cutoff with merge.raw.cluster.args; passes check except for 2 warnings unrelated to hc.cutoff, which I cannot figure out how to silence.

[ 2.0.1 ]

• Added pointers to the paper on bioRxiv

[ 2.0.0 ]

• Removing "frozen nodes" (still in branch "last-with-NR-frozen-nodes")

[ 1.2.7 ]

• Dependency on new version of hdpx

[ 1.2.6 ]

• Added more tests
• Major documentation cleanup
• Some function renaming
• Made some functions internal

[ 1.2.1 ]

• Removed "moderate" classification of confidence in aggregated clusters / signatures.
• Incremented version of hdpx required.
• Removed 'multi.types' from CombineChainsAndExtractSigs
• Add test for AnalyzeAndPlotretval
• Update some documentations

[ 1.2.0 ]

• Many changes

[ 1.1.4.9001]

• Improved error handling and reporting from mclapply child processes.

[1.0.2.003]

• MatchSigsAndRelabel was moved to ICAMSxtra

[0.0.0.9030] - 2020-07-14

• No longer necessary to checkpoint clean.chlist.Rdata

[0.0.0.9029] - 2020-07-13

• Added ability to specify parameters for gamma distribution prior on Dirichlet concentration parameters for the top level Dirichlet process node.

[0.0.0.9023] - 2020-06-27

• Added some checkpointing facilities in MultipleSetupAndPosterior and RunHdpParallel.

[0.0.0.9015]- 2020-06-06

• Stable version with package source file available to download for installation. See README.md for more details.

[0.0.0.9005]- 2020-05-16

• Changed arg for Runhdp4 and RundAndEvalHdp4 from input.catalog.file to input.catalog; starting to retire Runhpd5, RunAndEvalHdp5, RunhdpInternal5.
• Added reference manual and README.
• Updated DESCRIPTION to include biocViews and Imports as field name.
• Fixed typos and updated WORDLIST for spelling check.
• Added test data for test-RunhdpInternal4-fast-2types.R.
• Fixed a bug in test-RunhdpInternal4-slow.R.

[0.0.0.9004]- 2020-05-15

• Still trying to make the code robust to errors in mclapply children run hdp_posterior.

steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.