Find best fitting solutions for each sample
FindRascalSolutions.RdFindRascalSolutions() finds the best ploidy and cellularity pairs from the relative copy number profiles of each sample. Makes use of the find_best_fit_solutions() function from rascal.
Usage
FindRascalSolutions(
cnobj,
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
)Arguments
- cnobj
An S4 object of type QDNAseqCopyNumbers.
- 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
TRUEto return all solutions but with additionalbest_fitcolumn to indicate which are the local minima that are acceptable solutions (may be useful to avoid computing the distance grid twice)