silhouetteRankTest

Source: R/spatial_genes.R

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
)

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