NEWS

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cbaf 1.28.0 (2024-10-24)

New Features

• Introducing a new two step procedure for processMultipleStudies! If you intend to download the required data on server, CBAF can download and create a database, then it compress the database into a ZIP file. User can then transfer the zipped file into their local computer and CBAF can use that ZIP file to recreate the intial database that it needs. Since servers usually lack any graphical units, CBAF won't be able to generate heatmaps when running on server.

cbaf 1.20.0 (2022-10-24)

New Features

• Introducing oneOfEach! using this option would force the availableData() to return one study for each cancer type that contain a technique of interest, instead of storing all the data in an excel file.
• It is now possible to generate Heatmap for a single gene.

cbaf 1.18.0 (2022-04-24)

New Features

• Packge now uses cBioPortalData package to communicate with cBioPortal, as cgdsr package is deprecated.
• Package now supports RNA-seq data with z-scores relative to normal samples.
• Terms updated.
• Minor improvemets

cbaf 1.16.0 (2021-10-14)

New Features

• Terms updated.

cbaf 1.14.0 (2021-04-28)

New Features

• Heatmaps can now be stored as PDF files.
• Functions now show shorter and more clearer messages.
• Package no longer requires Java Runtime Environment for storing excel files and it is compatible with older 32 bit operating systems.
• log z-scores provided by cgdsr are used instead of z-scores.

cbaf 1.12.0 (2020-10-26)

New Features

• Terms are updated. Package can recongize even more cancer studies!
• Improvements for methylation analysis.
• If desired genes are entered as a vector, they are converted to a list without returning an error.

cbaf 1.10.0 (2020-04-08)

New Features

• A unified method for increasing the consistency of cancer terms used by various functions. This enables easier maintanance and faster inclusion of new terms whenever available.
• Terms are updated. Package can recongize even more cancer studies!
• Incluion of additional checkpoint to control the name of requested cancer studies.

cbaf 1.8.0 (2019-10-28)

New Features

• Optimization has led obtainOneStudy() and obtainMultipleStudies() functions to work faster.
• If an entered cancer has corrupted data or lacks the requested data type, obtainMultipleStudies() doesn't return error. That study is automatically omitted from results and its name is printed on console.
• AvailableData() function now works more accurately but unfortunately, it is generally slower: Due to inconsistancy in the terms that cgdsr uses, AvailableData() has to check the availability of the data at two different levels.

cbaf 1.6.0 (2019-04-28)

New Features

• heatmapOutput now uses a more accurate algorithm for determining the margins.
• Terms are updated. Package can recongize more cancers!

cbaf 1.4.0 (2018-10-30)

New Features

• obtainOneStudy() and obtainMultipleStudies() functions can obtain data for groups of genes each possess more than 250 genes (Virtually unlimited gene number).
• A new argument for xlsxOutput() function to exchange the columns and rows.

cbaf 1.2.0 (2018-04-26)

New Features

• heatmapOutput() can now determine the heatmap margines and column and row name sizes automatically.
• New image formats TIFF, JPG and BMP in addition to the previous PNG file format for heatmapOutput(). They can be chosen from processOneStudy() and processMultipleStudies or directly from heatmapOutput() function.
• heatmapOutput() now uses two methods for ranking the genes prior to generating heatmap(s). One of them is suited for finding genes that have unique high values in one or few cancer studies whereas the other method aids in detemining genes that possess high values in multiple / many cancers.
• If function argumnets are entered wrongly, more meaningful errors will appear.
• All functions are improved.

cbaf 1.0.0 (2017-09-10)

New Functions

• New availableData() functon to scan all the cancer studies to examine presence of RNA-seq, microRNA-seq, microarray(mRNA), microarray(miRNA) and methylation data.
• New obtainOneStudy() function to obtain and store the supported data for at least one group of genes across multiple subgroups of a cancer study. In addion, it can check whether or not all genes are included in different subgroups of a cancer study and, if not, looks for the alternative gene names.
• New obtainMultipleStudies() function to obtain and store the supported data for at least one group of genes across multiple cancer studies. It can check whether or not all genes are included in each cancer study and, if not, it looks for the alternative gene names.
• New automatedStatistics() function to calculate the statistics of the data obtained by obtainOneStudy() or obtainMultipleStudies() functions. Based on user's preference, these statistics can include frequency percentage, frequency ratio, mean value and median value of samples greater than specific value. Furthermore, it can look for the genes that comprise the highest values in each cancer and list the top 5 genes for frequency percentage, mean value and median value.
• New heatmapOutput() function to prepare heatmap for frequency percentage, mean value and median value data provided by automatedStatistics() function. Heatmaps for every gene group are stored in separate folder.
• New xlsxOutput() function to export the output of automatedStatistics() and the gene validation result of one of the obtainOneStudy() or obtainMultipleStudies() functions as an excel file. For every gene group, an excel file will be generated and stored in the same folder as heatmaps.
• New cleanDatabase() function to remove the created databases in the cbaf package directory. This helps users to obtain the fresh data from cbioportal.org.
• New processOneStudy() function to combine obtainOneStudy(), automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease of use.
• New processMultipleStudies() function to combine obtainMultipleStudies(), automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease of use.