sigs {YAPSA} | R Documentation

## Data for mutational signatures

### Description

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`

### Usage

    data(sigs)

### Author(s)

Daniel Huebschmann huebschmann.daniel@googlemail.com

### Source

`AlexInitial`: ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/signatures.txt

`AlexCosmic`: http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt

### References

Alexandrov et al. (Nature 2013)

[Package YAPSA version 1.18.0 Index]