Function that will fit a clonal copy number profile to segmented data. It first matches the raw LogR with the segmented BAF to create segmented LogR. Then ASCAT is run to obtain a clonal copy number profile. Beyond logRsegmented it produces the rho_and_psi file and the cellularity_ploidy file.
fit.copy.number(
samplename,
outputfile.prefix,
inputfile.baf.segmented,
inputfile.baf,
inputfile.logr,
dist_choice,
ascat_dist_choice,
min.ploidy = 1.6,
max.ploidy = 4.8,
min.rho = 0.1,
max.rho = 1,
min.goodness = 63,
uninformative_BAF_threshold = 0.51,
gamma_param = 1,
use_preset_rho_psi = F,
preset_rho = NA,
preset_psi = NA,
read_depth = 30,
analysis = "paired",
nthreads,
enhanced_grid_search = F
)Samplename used to name the segmented logr output file
Prefix used for all output file names, except logRsegmented
Filename that points to the BAF segmented data
Filename that points to the raw BAF data
Filename that points to the raw LogR data
The distance metric that is used internally to rank clonal copy number solutions
The distance metric used to obtain an initial cellularity and ploidy estimate
The minimum ploidy to consider (Default 1.6)
The maximum ploidy to consider (Default 4.8)
The minimum cellularity to consider (Default 0.1)
The maximum cellularity to consider (Default 1.0)
The minimum goodness of fit for a solution to have to be considered (Default 63)
The threshold beyond which BAF becomes uninformative (Default 0.51)
Technology parameter, compaction of Log R profiles. Expected decrease in case of deletion in diploid sample, 100 "%" aberrant cells; 1 in ideal case, 0.55 of Illumina 109K arrays (Default 1)
Boolean whether to use user specified rho and psi values (Default F)
A user specified rho to fit a copy number profile to (Default NA)
A user specified psi to fit a copy number profile to (Default NA)
Legacy parameter that is no longer used (Default 30)
A String representing the type of analysis to be run, this determines whether the distance figure is produced (Default paired)