Function reference
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tumopp()
make_args()
- Run tumopp
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make_igraph()
subtree()
internal_nodes()
- Functions depending on igraph
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propagate_drivers()
- Functions to deal with driver mutations
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sample_uniform_regions()
sample_random_regions()
sample_bulk()
evaluate_mrs()
distances_mrs()
- Sample cells from a population
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dist_genealogy()
dist_vaf()
pairwise_distances()
- Calculate genetic distance from genealogy or VAF
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make_vaf()
make_longer_vaf()
longer_vaf()
filter_detectable()
sort_vaf()
- Utilities for variant allele frequency
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make_sample()
- Sprinkle mutations on genealogy
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fst()
gst()
pairwise_fst()
- Calculate F_ST from matrix
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combn_ids()
summarize_capture_rate()
- Sample cells from a population
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extract_history()
summarize_demography()
- Functions for event history
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filter_extant()
count_extant()
filter_common_ancestors()
- Functions to modify population data.frame
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math_score()
- Evaluate heterogeneity
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genetic_stats()
morphological_stats()
- Summarizing functions
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stats_dispersion()
summary_row()
mutate_chisq()
rpois_dispersion()
tibble_dchisq()
- Utilities for dispersion
summary_row()
andmutate_chisq()
calculate various dispersion stats.stats_dispersion()
is a shortcut to call them both at once.
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max_abs_xyz()
dist_euclidean()
transform_rotate()
- Utilities for coordinate values
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trans_coord_hex()
- Transform coordinates into hexagonal grid
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add_surface()
add_phi()
- Extract surface cells with mathematical morphology
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as_cuboid()
as.data.frame(<cuboid>)
as.array(<cuboid>)
- Binary expression of cell existence
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augment_genealogy()
gggenealogy()
- Visualize cell genealogy
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plot_capture_rate()
- Plot capture_rate ~ nsam of biopsy
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plot_tumor3d()
snapshot_surface()
add_col()
- 3D plotting with rgl
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histogram_freqspec()
plot_lattice2d()
- ggplot for frequency spectrum
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save_serial_section()
- Plot serial sections of 3D tumor
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read_confs()
read_results()
read_tumopp()
- Read TSV files in given directories
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write_results()
- Utilities for writing files
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tumopp_path()
tumopp_version()
- Get the path to the tumopp installation.