filter Giotto object based on expression threshold
filterGiotto(
gobject,
expression_values = c("raw", "normalized", "scaled", "custom"),
expression_threshold = 1,
gene_det_in_min_cells = 100,
min_det_genes_per_cell = 100,
verbose = F
)
giotto object
expression values to use
threshold to consider a gene expressed
minimum # of cells that need to express a gene
minimum # of genes that need to be detected in a cell
verbose
giotto object
The function filterCombinations
can be used to explore the effect of different parameter values.
data(mini_giotto_single_cell)
filtered_gobject = filterGiotto(mini_giotto_single_cell,
gene_det_in_min_cells = 10,
min_det_genes_per_cell = 10)