Description Usage Arguments Value Examples
Find best fit solutions for a grid-based search through the given ranges of ploidies and cellularities.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | find_best_fit_solutions(
relative_copy_numbers,
weights = NULL,
min_ploidy = 1.5,
max_ploidy = 5.5,
ploidy_step = 0.01,
min_cellularity = 0.2,
max_cellularity = 1,
cellularity_step = 0.01,
distance_function = c("MAD", "RMSD"),
distance_filter_scale_factor = 1.25,
max_proportion_zero = 0.05,
min_proportion_close_to_whole_number = 0.5,
max_distance_from_whole_number = 0.15,
solution_proximity_threshold = 5,
keep_all = FALSE
)
|
relative_copy_numbers |
a numeric vector containing relative copy numbers, i.e. ratios of copy numbers to the average copy number. |
weights |
a numeric vector of weights to apply to each copy number value (should be same length as relative_copy_numbers) |
min_ploidy, max_ploidy |
the range of ploidies. |
ploidy_step |
the stepwise increment of ploidies along the grid. |
min_cellularity, max_cellularity |
the range of cellularities. |
cellularity_step |
the stepwise increment of cellularities along the grid. |
distance_function |
the distance function to use, either "MAD" for the mean absolute difference or "RMSD" for the root mean square difference, where differences are between the fitted absolute copy number values and the nearest whole number. |
distance_filter_scale_factor |
the distance threshold above which solutions will be discarded as a multiple of the solution with the smallest distance. |
max_proportion_zero |
the maximum proportion of fitted absolute copy number values in the zero copy number state. |
min_proportion_close_to_whole_number |
the minimum proportion of fitted absolute copy number values sufficiently close to a whole number. |
max_distance_from_whole_number |
the maximum distance from a whole number that a fitted absolute copy number can be to be considered sufficiently close. |
solution_proximity_threshold |
how close two solutions can be before one will be filtered; reduces the number of best fit solutions where there are many minima in close proximity. |
keep_all |
set to |
the distance in the fitted absolute copy numbers to whole numbers.
1 2 3 4 5 6 7 8 9 | data(copy_number)
copy_number <- copy_number[copy_number$sample == "X17222", ]
segments <- copy_number_segments(copy_number)
solutions <- find_best_fit_solutions(
segments$copy_number, segments$weight,
min_ploidy = 1.5, max_ploidy = 5.5,
distance_function = "MAD")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.