Wrapper to find Signature Exposures for a set of samples
CallSignatureExposures.RdCallSignatures() calculates copy-number signature exposures for a list of samples given their segmented copy-number profiles. This function makes use of code found in the CN-Signatures bitbucket repo. and described more robustly here https://www.nature.com/articles/s41588-018-0179-8.
Usage
CallSignatureExposures(
copy_numbers_input,
component_models = NULL,
signatures = NULL,
cores = 1,
log_features = FALSE,
extra_features = FALSE,
plot_savepath = NULL,
sigs_savepath = NULL,
relative = FALSE,
refgenome = "hg19"
)Arguments
- copy_numbers_input
A list of dataframes. Each dataframe should be the segmented copy-numbers of a sample.
- component_models
String. The mixture models to use in determining the components present in this dataset.
Options:
'component_models/30kb_ovarian/component_models_britroc_aCNs.rds' - Components determined by modelling the Britroc Ovarian sWGS samples. (Macintyre 2018)
'vancouver_HQendo_VAFrascal' - Components determined by modelling high-quality p53abn sWGS endometrial samples. (2022)- signatures
String. The signatures themselves. Please name those for which to calculate exposures.
Options:
'signatures/30kb_ovarian/component_by_signature_britroc_aCNs.rds' - The signatures created using the Britroc Ovarian sWGS samples. (Macintyre 2018)
'VAFrascalHQendoVan6sigs' - The signatures created using the high-quality p53abn sWGS endometrial samples.- plot_savepath
(optional) String. The path where to save a sample-by-component heatmap. Please provide a directory.
- sigs_savepath
(optional) String. The path where to save a csv of the calculated signature exposures. Please provide a directory.
- relative
(optional) Logical. If using relative Copy-Number data as input, set to TRUE. Otherwise, ignore.
- refgenome
(optional) String. The reference genome used. (ex. 'hg19', or 'hg38')
- data_path
String. The path where to find signatures objects and component models.