Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted
Source:R/discovery_prediction.R
combine_predict_grid.RdCombine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted
combine_predict_grid(grid_list, musica, table_name, signature_res)Arguments
- grid_list
A list of result objects from the prediction grid to combine into a single result
- musica
A
musicaobject.- table_name
Table name used for prediction
- signature_res
Signatures to automatically subset from for prediction
Value
A result object combining all samples and signatures from a prediction grid. Samples have zero exposure value for signatures not found in that annotation type.
Examples
data(musica_annot)
data(cosmic_v2_sigs)
grid <- auto_predict_grid(musica_annot, "SBS96", cosmic_v2_sigs, "lda",
"Tumor_Subtypes", combine_res = FALSE)
#> Lung
#> Breast
combined <- combine_predict_grid(grid, musica_annot, "SBS96", cosmic_v2_sigs)
plot_exposures(combined, group_by = "annotation",
annotation="Tumor_Subtypes")
