silhouetteRankTest

Multi parameter aggregator version of silhouetteRank

silhouetteRankTest(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  subset_genes = NULL,
  overwrite_input_bin = TRUE,
  rbp_ps = c(0.95, 0.99),
  examine_tops = c(0.005, 0.01, 0.05, 0.1, 0.3),
  matrix_type = "dissim",
  num_core = 4,
  parallel_path = "/usr/bin",
  output = NULL,
  query_sizes = 10L,
  verbose = FALSE,
  return_gobject = F
)

Arguments

gobject

giotto object

expression_values

expression values to use

subset_genes

only run on this subset of genes

overwrite_input_bin

overwrite input bin

rbp_ps

fractional binarization thresholds

examine_tops

top fractions to evaluate with silhouette

matrix_type

type of matrix

num_core

number of cores to use

parallel_path

path to GNU parallel function

output

output directory

query_sizes

size of query

verbose

be verbose

Value

data.table with spatial scores