From a cohort object, this function extracts the tree
objects that are available for a patient. Parameters
can be set to retrieve a particular tree, or the fit
tree which is however availble only after fitting the
cohort data. This function can either return a
phylogenetic clone tree (R object ctree), or mutation
trees (R object btree). Besides, it can return
the information transfer as the ordering of the annotated
drivers, or in terms o the ordering of the clones these
map to.
ITransfer(x, p, rank = 1, type = "drivers", data = "trees")
| x | A |
|---|---|
| p | The id of a patient in the cohort. |
| rank | The rank of the tree to extract. |
| type | Either `drivers` or `clones`. |
| data | Either `trees` or `fit`, which requires to have already computed the fit of the input cohort. |
The information transfer for the tree of a patient
Other Getters:
CCF_clusters(),
CCF(),
Clonal_cluster(),
Data(),
Drivers(),
Phylo(),
Samples(),
Subclonal(),
Truncal(),
get_features()
# Data released in the 'evoverse.datasets' data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets') # Get the transfer among drivers, top-ranking tree ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'drivers')#> # A tibble: 11 x 2 #> from to #> <chr> <chr> #> 1 MET RB1 #> 2 MET IKZF1 #> 3 MET KRAS #> 4 TERT RB1 #> 5 TERT IKZF1 #> 6 TERT KRAS #> 7 GL MET #> 8 GL TERT #> 9 EP300 NF1 #> 10 MET EP300 #> 11 TERT EP300# Get the transfer among clones, top-ranking tree ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'clones')#> # A tibble: 4 x 2 #> from to #> <chr> <chr> #> 1 2 1 #> 2 GL 2 #> 3 6 5 #> 4 2 6# Get the transfer from the fit ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'clones', data = 'fits')#> # A tibble: 4 x 2 #> from to #> <chr> <chr> #> 1 2 1 #> 2 GL 2 #> 3 6 5 #> 4 2 6ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'drivers', data = 'fits')#> # A tibble: 7 x 2 #> from to #> <chr> <chr> #> 1 GL MET #> 2 MET TERT #> 3 TERT EP300 #> 4 TERT RB1 #> 5 TERT IKZF1 #> 6 TERT KRAS #> 7 EP300 NF1