news.md

In steverozen/PCAWG7.WGS.Spectra: Repository of Data from paper 'The repertoire of Mutational Signatures in Human Cancer'

PCAWG7 0.1.3

• Removed the following exported data and functions as they are moved to another package cosmicsig:
• COSMIC.v3.2
• COSMIC.v3.1
• COSMIC.v3.0
• signature
• etiologies
• GetEtiology

• SBS96_ID_to_SBS192_ID

• Removed tests\testthat\test_GetEtiology.R

• Removed tests\testthat\test_SBS96_ID_to_SBS192_ID.R

• Updated documentation

PCAWG7 0.1.1.9006

• Added new exported data COSMIC.v3.2 and documentation

PCAWG7 0.1.1.9005

• Renamed internal data sigs.etiologies to etiologies and made it exported

PCAWG7 0.1.1.9004

• Moved ICAMS package to Suggests filed in DESCRIPTION and updated code to use the package conditionally

• Moved some obsolete code in SignatureExposureInfo.R to data-raw/old.code

PCAWG7 0.1.1.9003

• Improved time performance for function map_aliquot_ID_to_SP_ID and added Note section in documentation. Return NA with a warning for those aliquot IDs that cannot be matched to any "SP" IDs

PCAWG7 0.1.1.9002

• Fixed typo in SBS96 signature etiologies table

PCAWG7 0.1.1.9001

• Added new exported data PCAWG.sample.sheet, COSMIC.v3.1

• Added new exported function map_aliquot_ID_to_SP_ID

• Updated exported data signature from COSMIC v3.2 website and added signature etiologies data for new signatures

• Updated description for package documentation

PCAWG7 0.1.0.9006

• Corrected typos in data sigs.etiologies for SBS6 and SBS44

PCAWG7 0.1.0.9005

• Removed "SBS84" "SBS85" "SBS86" "SBS87" "SBS89" from internal data sigs.etiologies$SBS192

PCAWG7 0.1.0.9004

• Added new exported function TCGA_ID_to_ICGC_ID to translate TCGA(The Cancer Genome Atlas) IDs to ICGC(International Cancer Genome Consortium) IDs

• Added internal data TCGA.ICGC.IDs

PCAWG7 0.1.0.9003

• Added new exported function CancerTypes for returning a character vector of some common cancer types

PCAWG7 0.1.0.9002

• Added more examples and tests for exported data and functions

PCAWG7 0.1.0.9001

• Adapted SplitMatrixBySampleType to work with ICAMS catalogs and added tests
• Made ICAMS an Imports (because needed for the classes of the spectra and signature package variables)

PCAWG7 0.1.0.9000

• Non-backward-compatible: Removed package variables PCAWG.WGS.SBS.96 and PCAWG.WGS.DBS.
• Non-backward-compatible: made former COSMIC.v3.1$signature into signature, and made former signature into COSMIC.v3.0$signature

PCAWG7 0.0.3.9006

• Added new exported data COSMIC.v3.1 which contain the latest signatures from COSMIC website.

PCAWG7 0.0.3.9004

• Added indels and DBSs to exposure.stats and improved documentation.

PCAWG7 0.0.3.9003

• Working toward adding package variable exposure.stats

PCAWG7 0.0.3

• Added package man page.
• Added more plots to data-raw/plots/

PCAWG7 0.0.2

• Fully populated and documented exposure and spectra
• All changes backward compatible

PCAWG7 0.0.0.9006

• Corrected ID signatures; they were totally wrong.
• Made sure abundances were present where possible in signatures.

PCAWG7 0.0.0.9004

• Added indel (ID) signatures.
• Removed BSgenome objects as reference genomes (causing problems in clients).

steverozen/PCAWG7.WGS.Spectra documentation built on Jan. 27, 2022, 4:51 a.m.