filterGiotto
¶
filterGiotto
Description¶
filter Giotto object based on expression threshold
Usage¶
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
)
Arguments¶
Argument |
Description |
---|---|
|
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 |
Details¶
The function ``filterCombinations` <#filtercombinations>`_ can be used to explore the effect of different parameter values.
Value¶
giotto object
Examples¶
data(mini_giotto_single_cell)
filtered_gobject = filterGiotto(mini_giotto_single_cell,
gene_det_in_min_cells = 10,
min_det_genes_per_cell = 10)