filterGiotto#
Last Updated: Nov 17, 2023
Description#
filter Giotto object based on expression threshold
Usage#
filterGiotto(
gobject,
spat_unit = NULL,
feat_type = NULL,
expression_values = c("raw", "normalized", "scaled", "custom"),
expression_threshold = 1,
feat_det_in_min_cells = 100,
gene_det_in_min_cells = NULL,
min_det_feats_per_cell = 100,
min_det_genes_per_cell = NULL,
all_spat_units = TRUE,
all_feat_types = TRUE,
poly_info = "cell",
tag_cells = FALSE,
tag_cell_name = "tag",
tag_feats = FALSE,
tag_feats_name = "tag",
verbose = TRUE
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
expression values to use |
|
threshold to consider a gene expressed |
|
minimum # of cells that need to express a feature |
|
deprecated, use feat_det_in_min_cells |
|
minimum # of features that need to be detected in a cell |
|
deprecated, use min_det_feats_per_cell |
|
apply features to remove filtering results from current spatial unit/feature type combination across ALL spatial units (default = TRUE) |
|
apply cells to remove filtering results from current spatial unit/feature type combination across ALL feature types (default = TRUE) |
|
polygon information to use |
|
tag filtered cells in metadata vs. remove cells |
|
column name for tagged cells in metadata |
|
tag features in metadata vs. remove features |
|
column name for tagged features in metadata |
|
verbose |
Details#
The function filterCombinations
can be used to explore the effect of
different parameter values.
Value#
giotto object