NEWS.md

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

ICAMS 2.3.10

Added

• Added tolerance when using expect_equal for comparing numerical values

ICAMS 2.3.9

Fixed

• Updated some tests for TransformCatalog in case R was configured and built in a way that did not support long double.

Added

• Added back URLs for information regarding ID classification and SigProfiler catalog format.

ICAMS 2.3.8

Fixed

• Removed some URLs in README.md and some function documentations as they were identified as (possibly) invalid URLs by CRAN.

Changed

• Updated documentation of ReadCatalog and ReadCatalogInternal as there are no ID96 catalogs in COSMIC v3.2.

• Changed the URL of COSMIC mutational signatures page to the redirected URL.

ICAMS 2.3.7

Fixed

• Removed some URLs in README.md and some function documentations as they were identified as (possibly) invalid URLs by CRAN.

ICAMS 2.3.6

Fixed

• Updated some tests for TransformCatalog in case R was configured and built in a way that did not support long double.

• Added the argument strict back to ReadCatalog for backward compatibility; strict is now ignored and deprecated.

• Robustified function StandardChromNameNew to select the column which contains chromosome names by name instead of column index.

• Fixed a bug in function CheckSeqContextInVCF.

• Fixed a bug in function PlotCatalog.SBS96Catalog when plotting the X axis after setting par(tck) = 0.

Changed

• Changed PlotCatalog to round the mutation counts for each main type for SBS96, SBS192, DBS78 and ID counts catalog in case the input is reconstructed counts catalog.

• Updated function AdjustNumberOfCores not to throw a message on MS Windows machine.

Added

• Added an additional argument ylabels to PlotCatalog and PlotCatalogToPdf. When ylabels = FALSE, don't plot the y axis labels. Implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.

• Enabled argument grid, uppder, xlabels in PlotCatalog and PlotCatalogToPdf for DBS78Catalog, IndelCatalog.

ICAMS 2.3.5

Added

• Enabled function ReadCatalog to import files with:
• SigProfiler-formatted SBS96, DBS78, ID83 and ID96 catalogs.
• COSMIC-formatted SBS96, SBS192 (a.k.a. TSB192), DBS78, ID83 and ID96 catalogs.
• ID96 catalog files in SigProfiler/COSMIC format will be pruned to ID83 catalogs by removing mutation types not in ID83 catalogs.

Deprecated

• Deprecated internal methods of ReadCatalog function, e.g. ReadCatalog.SBS96Catalog. Now they are in data-raw/obsolete-files/ReadCatalogMethods.R.
• Deprecated function ConvCatalogToICAMS to convert SigProfiler/COSMIC-formatted catalog files into ICAMS catalog objects. Now these functions are in data-raw/obsolete-files/ConvCatalogToICAMS.R, and their functionalities are integrated into ReadCatalog.

ICAMS 2.3.4

Fixed

• Robustified function ReadCatalog to remove rows which have NA in the data table read in. Otherwise the number of rows will not be accurate to infer the correct catalog type.

Added

• Added new COSMIC catalog in testdata.

Removed

• Removed internal function InferClassOfCatalogForRead to data-raw/obsolete-files/InferClassOfCatalogForRead.R.

ICAMS 2.3.3

Fixed

• Fixed a bug in function CreateOneColDBSMatrix when returning 1-column DBS144 matrix with all values being 0 and the correct row labels.

Changed

• Increased sample name y axis position for plotting ID counts signature.

ICAMS 2.3.2

Added

• Added an additional argument tmpdir in function AddRunInformation.

• Updated function CheckAndRemoveDiscardedVariants and MakeDataFrameFromVCF to check for variants that have same REF and ALT.

Fixed

• Create new temp directory when generating zip archive from VCFs to avoid zipping unnecessary files in the output.

• Fixed a bug in function AddRunInformation for allowing ref.genome to be a Bioconductor package.

• Fixed bugs in function CreateOneColSBSMatrix, CreateOneColDBSMatrix and CreateOneColIDMatrix when the variants in the input vcfs should all be discarded.

Changed

• Updated function CheckAndFixChrNames to give a warning instead of an error when "23" and "X" or "24" and "Y" appear on the chromosome names on the VCF at the same time. CheckAndFixChrNames will change "23" to "X" or "24" to "Y" internally for downstream processing.

• Changed some code in function AddTranscript, CreateOneColSBSMatrix, CreateOneColDBSMatrix to use functions from package dplyr instead of data.table due to segfault error.

Updated

• Updated function RemoveRowsWithDuplicatedCHROMAndPOSNew to remove variants that have same CHROM, POS, REF.

ICAMS 2.3.1

Added

• Added an optional argument files in function VCFsToZipFile.

Fixed

• Fixed a bug in ReadAndSplitVCFs for merging adjacent SBSs into DBS when variant.caller is mutect.

• Fixed a bug inCheckAndRemoveDiscardedVariants for removing wrong DBS variants.

Updated

• Updated function CheckAndRemoveDiscardedVariants to remove wrong DBS variants that have same base in the same position in REF and ALT (e.g. TA > TT or GT > CT).

Changed

• Changed plotting function for IndelCatalog to adjust the sample name position when the catalog type is counts.

ICAMS 2.3.0

Added

• Added an additional argument name.of.VCF in function MakeDataFrameFromVCF for better error reporting.

Changed

• Changed plotting function for DBS78Catalog, SBS192Catalog to adjust the sample name position when the catalog type is counts.

Updated

• Updated function MakeDataFrameFromVCF for better error reporting when reading in files that are actually not VCFs.

• Updated function ReadVCFs to automatically change the number of cores to 1 on Windows instead of throwing an error.

Fixed

• Fixed a bug in CheckAndFixChrNames for returning the correct number of chromosome names.

Removed

• Removed argument stop.on.error and code tryCatch in function VCFsToCatalogs for better tracing if the function stops on error.

ICAMS 2.2.8

Added

• Added argument stop.on.error to VCFsToCatalogs; if false, return list with single element named error.

• Added new internal function CheckAndFixChrNamesForTransRanges. The chromosome names in exported data TranscriptRanges don't have "chr". ICAMS now will check for the chromosome names format in input vcf and update the trans.ranges chromosome names in function AddTranscript if needed.

• Added new argument name.of.VCF in function AnnotateSBSVCF and AnnotateDBSVCF for better error reporting.

• Changed return from ReadCatalog to include possible attribute "error" and allow for not calling stop() on error.

• For a stranded catalog, as.catalog and ReadCatalog will silently convert region = "genome" to "transcript".

Updated

• Updated function AddTranscript to check whether the format of VCF chromosome names is consistent with that in trans.ranges used.

• Removed documentation warnings related to \link{BSgenome...}

• Some file reorganization.

Fixed

• Fixed a bug in CreateOneColSBSMatrix for showing message that SBS variant whose reference base in ref.genome does not match the reference base in the VCF file.

ICAMS 2.2.7

Added

• Enabled functions PlotCatalog and PlotCatalogToPdf to plot a numeric matrix, numeric data.frame, or a vector denoting the mutation counts.

• Added new internal function AdjustNumberOfCores to change the number of cores automatically to 1 if the operating system is Windows.

• Added test processing VCF with unknown variant caller.

Changed

• Updated plotting function for SBS96Catalog to adjust the sample name position when the catalog type is counts.

ICAMS 2.2.6

Added

• Added new internal function SplitSBSVCF, SplitOneVCF, SplitListOfVCFs and VCFsToZipFileXtra, WriteSBS96CatalogAsTsv, ReadSBS96CatalogFromTsv, GetConsensusVAF.

• Added new exported function ReadAndSplitVCFs, VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and VCFsToZipFile.

• Added new argument filter.status and get.vaf.function in functions ReadVCF, ReadVCFs, ReadAndSplitVCFs, VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and VCFsToZipFile.

• Added a new internal data catalog.row.headers.SBS.96.v1.

• Added new argument max.vaf.diff in internal functions SplitOneVCF, SplitListOfVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and VCFsToZipFile.

• Added new dependency package parallel.

• Added new dependency package R.utils for data.table::fread to read gz and bz2 files directly.

• Added new argument num.of.cores in internal functions ReadVCFs, SplitListOfVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogsAndPlotToPdf, VCFsToCatalogs, VCFsToZipFile, VCFsToIDCatalogs, VCFsToSBSCatalogs, VCFsToDBSCatalogs.

• Added new argument ... in internal functions ReadVCF, ReadVCFs and exported functions ReadAndSplitVCFs, VCFsToCatalogsAndPlotToPdf, VCFsToCatalogs, VCFsToZipFile.

• Added new argument mc.cores in internal functions GetConsensusVAF.

Changed

• Updated function MakeDataFrameFromVCF to use data.table::fread instead of read.csv.

Fixed

• Fixed bug in MakeDataFrameFromVCF when reading in VCF from URL.

ICAMS 2.2.5

Changed

• Updated function CreateOneColSBSMatrix to throw a message instead of an error when there are SBS variant whose reference base in ref.genome does not match the reference base in the VCF file.

• Updated function MakeVCFDBSdf to inherit column information from original SBS VCF.

• Changed the words in legend for DBS144 plot from "Transcribed", "Untranscribed" to "Transcribed strand" and "Untranscribed strand".

• Updated the documentation for exported data all.abundance.

• Updated function ReadCatalog.COMPOSITECatalog not to convert "::" to ".." in the column names.

• Updated various functions in ICAMS to generate catalogs with zero mutation counts from empty vcfs.

ICAMS 2.2.4 (submitted to CRAN)

Changed

• Updated the code in automated tests to use packages in Suggests conditionally as required by CRAN.

ICAMS 2.2.3 (submitted to CRAN)

Added

• Added a section "ID classification" in the documentation for exported data catalog.row.order.

• New argument suppress.discarded.variants.warnings in exported function AnnotateIDVCF with default value TRUE.

• Added another paper information in AddRunInformation. "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types", Genome Research 2020 https://doi.org/10.1101/gr.255620.119.

Changed

• Changed the format of DOIs in DESCRIPTION according to CRAN policy.

• Changed back the return value of ReadStrelkaIDVCFs, ReadStrelkaSBSVCFs, ReadMutectVCFs to a list of data frames with no variants discarded.

• Combined all the discarded variants from ReadAndSplitMutectVCFs and ReadAndSplitStrelkaSBSVCFs under one element discarded.variants in the return value. An extra column discarded.reason were added to show the details.

• Updated internal functions ReadVCF and ReadVCFs not to remove any discarded variants.

• No more removal of "chr" in the CHROM column when reading in VCFs.

Fixed

• Fixed bugs in CheckAndReturnSBSMatrix, CheckAndReturnDBSMatrix, CreateOneColSBSMatrix,CreateOneColDBSMatrix, VCFsToSBSCatalogs, VCFsToDBSCatalogs.

ICAMS 2.2.2

Added

• Added a section "Frequently asked questions" in README.

Fixed

• Fixed a bug in CalculateExpressionLevel for the edge case.

ICAMS 2.2.1

Fixed

• Fixed a bug in CreateOneColIDMatrix when the ID.class contains non canonical representation of the ID mutation type.

ICAMS 2.2.0

Mostly backward compatible

• The return value of exported function ReadStrelkaIDVCFs now sometimes contains a new element, discarded.variants. This appears when there are variants that were discarded immediately after reading in the VCFs. At present these are variants that have duplicated chromosome/positions and variants that have illegal chromosome names. This means that the user must check the return to see if discarded.variants is present and remove it before passing the return to a function that expects a list of VCFs. Code in ICAMS that takes lists of VCFs already checks for this element and removes it if present.

• Added argument return.annotated.vcfs to exported function VCFsToIDCatalogs. The default value for the argument is FALSE to be consistent with other functions.

New function arguments with backward compatible defaults

• Argument return.annotated.vcfs in functions VCFsToSBSCatalogs,VCFsToDBSCatalogs, VCFsToIDCatalogs, MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf, MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToZipFile, StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf and StrelkaIDVCFFilesToZipFile.

• Argument suppress.discarded.variants.warnings in functions ReadAndSplitMutectVCFs, ReadAndSplitStrelkaSBSVCFs, VCFsToSBSCatalogs,VCFsToDBSCatalogs, VCFsToIDCatalogs, MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf, MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToZipFile, StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf and StrelkaIDVCFFilesToZipFile.

Documentation updates

• Added documentation to exported functions ReadAndSplitStrelkaSBSVCFs, StrelkaSBSVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogAndPlotToPdf and StrelkaSBSVCFFilesToZipFile.

• Added information on the "ID classification" in documentation of functions generating ID catalogs, FindDelMH and FindMaxRepeatDel.

• Minor changes to documentation of functions PlotCatalog, PlotCatalogToPdf, StrelkaSBSVCFFilesToZipFile, StrelkaIDVCFFilesToZipFile and MutectVCFFilesToZipFile.

• Updated documentation for the return value of functions StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf, StrelkaIDVCFFilesToZipFile and VCFsToIDCatalogs to make it clearer to the user.

Other backward compatible changes

• Added new exported data of catalog row order for SBS96, SBS1536 and DBS78 in SigProfiler format to catalog.row.order.sp.

• New internal function ConvertICAMSCatalogToSigProSBS96, ReadVCF, ReadVCFs.

• New exported function GetFreebayesVAF for calculating variant allele frequencies from Freebayes VCF.

• New test data for Strelka mixed VCF.

• Added time zone information to file "run-information.txt" when calling functions MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToZipFile and StrelkaIDVCFFilesToZipFile.

• Enabled "counts" -> "counts.signature" catalog transformation when the source catalog has NULL abundance.

• Added legend for SBS192 plot and changed the legend text for SBS12 plot.

• Added a second element plot.object to the return list from function PlotCatalog for catalog types "SBS192Catalog", "DBS78Catalog", "DBS144Catalog" and "IndelCatalog". The second element is a numeric vector giving the coordinates of the bar midpoints, useful for adding to the graph.

• Made the returns from PlotCatalog and PlotCatalogToPdf invisible.

• Improved time performance of GetMutectVAF, CanonicalizeDBS, CanonicalizeQUAD.

Fixed bugs in ...

• if statements in GetCustomKmerCounts、 GetStrandedKmerCounts and GetGenomeKmerCounts.

• CreateOneColIDMatrix when there is NA ID category.

• GetMutectVAF to check if the VCF is indeed a Mutect VCF.

• CreateOneColDBSMatrix when the VCF does not have any variant in the transcribed region.

• CalculatePValues when there is only a single expression value.

ICAMS 2.1.2 (submitted to CRAN)

Added

• Created an internal function MakeDataFrameFromVCF to read in data lines of a VCF.

• New argument name.of.VCF in internal function CheckAndFixChrNames to make the error message more informative.

• New argument name.of.VCF in exported function AnnotateIDVCF to make the error message more informative.

Changed

• Updated internal function ReadStrelkaIDVCF to make the error message more informative.
• (Non backward-compatible) Changed the return of exported function AnnotateIDVCF to a list. The first element annotated.vcf contains the annotated VCF. If there are rows that are discarded, the function will generate a warning and a second element discarded.variants will be included in the returned list.

Deprecated

• Argument flag.mismatches deprecated in exported function AnnotateIDVCF. If there are mismatches to references, the function will automatically discard these rows. User can refer to the element discarded.variants in the return value for the discarded variants.

Fixed

• Fixed a bug in internal function SplitStrelkaSBSVCF when there are no non.SBS mutations in the input.
• Fixed a bug in internal function MakeDataFrameFromMutectVCF when a Mutect VCF has no meta-information lines.
• Fixed a bug in internal function CreateOneColSBSMatrix when an annotated SBS VCF has variants on transcribed regions that all fall on transcripts on both strand.
• Fixed a bug in internal function CreateOneColDBSMatrix when an annotated DBS VCF has variants on transcribed regions that all fall on transcripts on both strand.

ICAMS 2.1.1

Added

• (New) Added columns of VAF (variant allele frequency) and read depth information to the split DBS.vcfs from merged SBSs when calling function ReadAndSplitStrelkaSBSVCFs.
• Added a new dependency package "zip" in ICAMS, to be used in three new exported functions MutectVCFFilesToZipFile, StrelkaSBSVCFFilesToZipFile and StrelkaIDVCFFilesToZipFile.
• Added code to handle multiple alternate alleles in Strelka VCFs, e.g cases where REF = T and ALT = A,C which indicates the alternate allele in some reads is A and in some reads C.
• Added an internal function to infer trans ranges from input ref.genome. Updated the documentation of the exported functions which have argument trans.ranges to make it optional.
• Added an additional argument name.of.VCF in internal functions ReadStrelkaSBSVCF, ReadStrelkaIDVCF and exported function GetStrelkaVAF.
• Added an optional argument flag.mismatches in functions VCFsToIDCatalogs, MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf, MutectVCFFilesToZipFile, StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf and StrelkaIDVCFFilesToZipFile.

Changed

• (Non backward-compatible) Changed the return of function GetStrelkaVAF and GetMutectVAF to a data frame which contains the VAF and read depth information.
• (Non backward-compatible) Made the return from function PlotCatalogToPdf a list. The first element is a logical value indicating whether the plot is successful. The second element is a list containing the strand bias statistics (only for SBS192Catalog with "counts" catalog.type and non-NULL abundance and argument plot.SBS12 = TRUE).
• Slight changes to behavior of PlotCatalog and PlotCatalogToPdf: For class SBS96Catalog: (New) Allow setting ylim and cex. (New) For PlotCatalog (not PlotCatalogToPdf), allow plotting of a 96 x 2 catalog, in which case behavior is a stacked bar chart. (New) Plot x axis tick marks if xlabels is not TRUE; set par(tck = 0) to suppress. For class IndelCatalog: (New) Allow setting ylim.
• Renamed internal function creating custom abundance to GetCustomKmerCounts.
• Updated documentation for optional arguments in the functions reading VCF files. Used @inheritParams to reduce repetitive documentation.
• Updated function PlotTransBiasGeneExpToPdf so that ymax on the plot will be changed based on plot.type.
• Changed the class of values in internal data flat.abundance from "numeric" to "integer".

Deprecated

• Deprecated counts -> counts transformation in TransformCatalog; see documentation for rationale.

Fixed

• Fixed a bug in function TransformCatalog and updated its documentation for parameter target.abundance.
• Fixed bugs in internal function CheckAndFixChrNames and updated the automated tests.
• Corrected error message in TransformCatalog.
• Fixed a bug in exported function GetMutectVAF and updated the warning message to make it more informative.
• Fixed bugs in functions generating zip archive from VCF files and added more automated test.
• Updated methods of different types of catalogs for the generic function cbind to check the attributes of the incoming catalogs and assign attributes accordingly.
• Updated function TransformCatalog to check the attributes of the catalog to be transformed in the first place.
• Fixed bugs in code removing complex indels.

ICAMS 2.0.10 (submitted to CRAN)

Added

• Added exported functions AnnotateSBSVCF, AnnotateDBSVCF and AnnotateIDVCF.
• Added two exported functions PlotTransBiasGeneExp and PlotTransBiasGeneExpToPdf.
• Added an additional optional argument names.of.VCFs in functions ReadAndSplitMutectVCFs, ReadAndSplitStrelkaSBSVCFs, ReadStrelkaIDVCFs, MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf, StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalog and StrelkaSBSVCFFilesToCatalogAndPlotToPdf for users to specify the names of samples in the VCF files.
• Added error checking on the order of rownames in the input of as.catalog.
• Added code to handle the case where the #CHROM lines appear interspersed with rows for variants in a Mutect VCF file.
• Added two exported package variables, gene.expression.data.HepG2 and gene.expression.data.MCF10A.
• Added an additional optional argument tumor.col.names in functions ReadAndSplitMutectVCFs, MutectVCFFilesToCatalog and MutectVCFFilesToCatalogAndPlotToPdf to specify the column of the VCF that contains sequencing statistics such as sequencing depth; this column is often called "unknown" in Mutect.
• Added a "Comments" section in the documentation of functions MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalog, StrelkaSBSVCFFilesToCatalogAndPlotToPdf, VCFsToSBSCatalogs, VCFsToDBSCatalogs, ReadCatalog informing the user how to change attributes of the generated catalog.

Changed

• (Non backward-compatible) Made the return from functions VCFsToIDCatalogs, StrelkaIDVCFFilesToCatalog and StrelkaIDVCFFilesToCatalogAndPlotToPdf a list; 1st element is the spectrum catalog (previously the only return); 2nd element is a list of VCFs with additional annotations.
• (Non backward-compatible) Made the return from function PlotCatalog a list. The first element is a logical value indicating whether the plot is successful. The second element is a numeric vector giving the coordinates of all the bar midpoints drawn, useful for adding to the graph (only implemented for SBS96Catalog).
• (Slightly Non backward-compatible) Changed the handling of the output.file argument in MutectVCFFilesToCatalogAndPlotToPdf, StrelkaSBSVCFFilesToCatalogAndPlotToPdf, and StrelkaIDVCFFilesToCatalogAndPlotToPdf so that an indicator of the catalog type plus ".pdf" is simply appended to the base output.file name. Also made this argument optional with sensible default behavior.
• Changed column name 'gene.name' to 'gene.symbol' and added Ensembl gene ID information in exported package variables trans.ranges.GRCh37, trans.ranges.GRCh38 and trans.ranges.GRCm38.
• In FindDelMH, cryptic repeats (i.e. un-normalized deletions in a repeat such as GAGG deleted from CCCAGGGAGGGTCCC, which should be normalized to a deletion of AGGG) are now ignored with a warning rather than causing a stop.
• Updated plotting functions to make y axis labels more informative.
• Updated splitting functions for Mutect VCF to detect and move complex indels to "other" category.

Fixed

• Updated methods so that they are compatible with new versions of R, in which the class of a matrix is c("matrix", "array").
• Fixed a rarely encountered bug in FindDelMH, which previously did not flag the cryptic repeat in what is now the second example in the function documentation.

ICAMS 2.0.9

Added

• as.catalog supports creation of the catalog from a vector (interpreted as a 1-column matrix) and optionally infers the class from the number of rows in the input.
• Exported some functions that are used in categorizing deletions as a way to make documentation of the underlying logic more visible.

ICAMS 2.0.8 (submitted to CRAN)

Added

• Added ability to calculate VAF from newer version Mutect VCF files.

Changed

• Moved two Bioconductor packages(BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg38) from Imports to Suggests so that they can be used conditionally in "ICAMS" as requested by CRAN.
• Documentation updates.

ICAMS 2.0.7 (submitted to CRAN)

Fixed

• Additional corrections for submission to CRAN (putting on.exit(par(opar)) immediately after opar <- par(...) in every case.

ICAMS 2.0.6

Fixed

• Additional changes for submission to CRAN (re-set graphics parameters to original values after plotting calls; documentation updates).

ICAMS 2.0.5

Added

• Added support for BSgenome.Mmusculus.UCSC.mm10.

Changed

• Changes in response to initial submission to CRAN.

ICAMS 2.0

• First stable release. Mutational catalogs are S3 classes.

ICAMS 1.0

• Only available on GitHub; interfaces not compatible with ICAMS 2.0.

ICAMS documentation built on April 3, 2021, 5:07 p.m.