NEWS

---

gcap 1.2.0

• Utilized the latest ASCAT version from VanLoo-lab/ascat for default copy number calling. This help address issue mentioned at #43.
• Updated documentation.
• Added a whole workflow for debugging purpose.
• Enhanced path parsing like ~.
• Fixed bug in gcap-bam.R.

gcap 1.1.4

• Removed the XGBOOST version limits, instead, a warning is posted.
• Used GitHub action to render pkgdown site.

gcap 1.1.3

• Updated the logic of using only_oncogenes for filtering.

gcap 1.1.2

• Fixed the data loading for oncogene of mouse.

gcap 1.1.1

• Updated Sequenza workflow.
• Fixed the re-handling of errored seqz and facets runs.

gcap 1.1.0

• Supported analysis workflow from FACETS and Sequenza.
• Mouse genome is enabled based on the two implemented workflows above.

gcap 1.0.0

• The first public and stable release.

gcap 0.21.0

• Corrected blood label to somatic (https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/523).

gcap 0.20.2

• Limited xgboost version lower than 1.6 as it will not keep some key info in .rds file.

gcap 0.20.1

• Enhance the getGeneSummary() and getCytobandSummary() methods to return mutation matrix.

gcap 0.20.0

• This version is not compatible with previous versions, as the analysis and visualization functions are moved to an independent package 'gcaputils'.

gcap 0.14

• Added some utils functions and visualization functions.

gcap 0.13

• Updated initial setting and CLI.

gcap 0.12

This version has been discarded from git history.

gcap 0.11.1

• Supported a NA passing as tightness to remove the use of TCGA blood summary data as a more strict threshold for circular amplicon.

gcap 0.11.0

• Added fCNA$subset() method.
• Added gcap.plotDistribution() function.

gcap 0.10.0

• Added gcap.plotForest().
• Added gcap.plotKMcurve().
• Added gcap.plotProfile().
• Added method convertGeneID() to fCNA class.
• Set a default value for pdata option in fCNA$new().

gcap 0.9.0

• Supported gcap as main command, and previous two commands as subcommands if GetoptLong version >=1.1.0. Note: not test yet.

gcap 0.8.1

• Cleaned logic.

gcap 0.8.0

• Added options tightness and gap_cn.
• Renamed gcap-wes.R script to gcap-bam.R.

gcap 0.7.0

• Handled void result.
• Updated the background copy number reference and criterion judging a amplicon (#22).

gcap 0.6.0

• Designed and implemented a class fCNA used for storing the workflow key outputs and downstream analysis and visualization.

gcap 0.5.0

• Provided a function convertID() to convert gene IDs.
• Optimized the output summary.
• Re-constructed scoring and workflow output.

gcap 0.4.1

• Added use_best_ntreelimit in gcap.runPrediction() to control the ntree setting. When it is FALSE, we use a custom processing to obtain a more conservative tree number.
• Added deploy() to auto-deploy the CLI to /usr/loca/bin.
• Added easy-to-use CLI in inst directory.
• Filled NAs to input when age and gender are not available.
• Automatically appended logs to specific directory with rappdirs::app_dir("gcap", "ShixiangWang"). Users can obtain log path and cat log info with gcap:::get_log_file() and gcap:::cat_log_file() for debugging. (#14)
• Supported XGB54 model in workflows. (#13)

gcap 0.4.0

• After exploration, we found our stepwise model outperform MBO tuned model. So the models for predicting circular target have been limited to 3.
• gcap.ASCNworkflow() now supports input with only total integer copy number, like the result from ABSOLUTE software (also DoAbsolute).
• Added stepwised model for circle target.
• Changed the way how to select model and run prediction.
• custom_model in gcap.runPrediction() has been changed to model. This is inconsistent with version below v0.4.

gcap 0.3.3

• Updated scoring for supporting different thresholds.
• Wrapped ASCAT workflow in tryCatch() to avoid abnormal failure.

gcap 0.3.2

• Fixed input extra_info sample (order) issues.

gcap 0.3.1

• Fixed the issue about rendering wrong data files when skipping existing ASCAT calling.

gcap 0.3.0

• Updated models for prediction.

gcap 0.2.1

• Removed prob_cutoff setting in workflows. Directly use prob 0.1, 0.5 and 0.9 for cutting low, medium and high quality amplicon.

gcap 0.2.0

• Implemented an alternative workflow from allele specific copy number data to final result files. (#5)

gcap 0.1.0

• Implemented basic workflow from BAM files to result files.
• Added a NEWS.md file to track changes to the package.