sigs: Data for mutational signatures
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Author(s) Source References

The numerical data of the mutational signatures published initially by Alexandrov et al. (Nature 2013) and Alexandrov et al., (Bioaxiv 2018) is stored in data frames with endings _sig_df, the associated meta-information is stored in data frames with endings _sigInd_df. There are several instances of _sig_df and _sigInd_df, corresponding to results and data obtained at different times and with different raw data. There always is a one-to-one correspondence between a _sig_df and a _sigInd_df. The data frames of type _sig_df have as many rows as there are features, i.e. 96 if analyzing mutational signatures of SNVs in a triplet context, and as many columns as there are signatures. Data frames of type _sigInd_df have as many rows as there are signatures in the corresponding _sig_df and several columns:

sig: signature name
index: corresponding to the row index of the signature
colour: colour for visualization in stacked barplots
process: asserted biological process
cat.coarse: categorization of the signatures according to the asserted biological processes at low level of detail
cat.medium: categorization of the signatures according to the asserted biological processes at intermediate level of detail
cat.high: categorization of the signatures according to the asserted biological processes at high level of detail
cat.putative: categorization of the signatures according to the asserted biological processes based on clustering and inference

Please note, that categorization columns are only present for the data frames corrosponding to the data from Alexandorv et al. (Nature 2013).

AlexInitialArtif_sig_df: Data frame of the signatures published initially by Alexandrov et al. (Nature 2013). There are 27 signatures which constitute the columns, 22 of which were validated by an orhtogonal sequencing technology. These 22 are in the first 22 columns of the data frame. The column names are A pasted to the number of the signature, e.g. A5. The nonvalidated signatures have an additional letter in their naming convention: either AR1 - AR3 or AU1 - AU2. The rownames are the features, i.e. an encoding of the nucleotide exchanges in their trinucleotide context, e.g. C>A ACA. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.

AlexInitialArtif_sigInd_df: Meta-information for AlexInitialArtif_sig_df

AlexInitialValid_sig_df: Data frame of only the validated signatures published initially by Alexandrov et al. (Nature 2013), corresponding to the first 22 columns of AlexInitialArtif_sig_df

AlexInitialValid_sigInd_df: Meta-information for AlexInitialValid_sig_df

AlexCosmicValid_sig_df: Data frame of the updated signatures list maintained by Ludmil Alexandrov at http://cancer.sanger.ac.uk/cosmic/signatures. The column names are AC pasted to the number of the signature, e.g. AC5. The naming convention for the rows is as described for AlexInitialArtif_sig_df.

AlexCosmicValid_sigInd_df: Meta-information for AlexCosmicValid_sig_df

AlexCosmicArtif_sig_df: Data frame of the updated signatures list maintained by Ludmil Alexandrov at http://cancer.sanger.ac.uk/cosmic/signatures and complemented by the artifact signatures from the initial publication, i.e. the last 5 columns of AlexInitialArtif_sig_df. The column names are AC pasted to the number of the signature, e.g. AC5. The naming convention for the rows is as described for AlexInitialArtif_sig_df.

AlexCosmicArtif_sigInd_df: Meta-information for AlexCosmicArtif_sig_df