find_common_diploid | R Documentation |
Find the common diploid region in a group of pseudobulks
find_common_diploid( bulks, grouping = "clique", gamma = 20, theta_min = 0.08, t = 1e-05, fc_min = 2^0.25, alpha = 1e-04, min_genes = 10, ncores = 1, segs_loh = NULL, debug = FALSE, verbose = TRUE )
bulks |
dataframe Pseudobulk profiles (differentiated by "sample" column) |
grouping |
logical Whether to use cliques or components in the graph to find dipoid cluster |
gamma |
numeric Dispersion parameter for the Beta-Binomial allele model |
theta_min |
numeric Minimum imbalance threshold |
t |
numeric Transition probability |
fc_min |
numeric Minimum fold change to call quadruploid cluster |
alpha |
numeric FDR cut-off for q values to determine edges |
ncores |
integer Number of cores to use |
list Ploidy information
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