filterGiotto: filterGiotto
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

filterGiotto

R Documentation

filterGiotto

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

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`expression_values`	expression values to use
`expression_threshold`	threshold to consider a gene expressed
`feat_det_in_min_cells`	minimum # of cells that need to express a feature
`gene_det_in_min_cells`	deprecated, use feat_det_in_min_cells
`min_det_feats_per_cell`	minimum # of features that need to be detected in a cell
`min_det_genes_per_cell`	deprecated, use min_det_feats_per_cell
`all_spat_units`	apply features to remove filtering results from current spatial unit/feature type combination across ALL spatial units (default = TRUE)
`all_feat_types`	apply cells to remove filtering results from current spatial unit/feature type combination across ALL feature types (default = TRUE)
`poly_info`	polygon information to use
`tag_cells`	tag filtered cells in metadata vs. remove cells
`tag_cell_name`	column name for tagged cells in metadata
`tag_feats`	tag features in metadata vs. remove features
`tag_feats_name`	column name for tagged features in metadata
`verbose`	verbose

Details

The function filterCombinations can be used to explore the effect of different parameter values. Please note that this function filters data in a predefined order, features, then cells. After filtering in this order, certain features may be left over in the metadata with a corresponding number of cells which is less than that of the threshold value of cells, feat_det_in_min_cells. This behavior is explained in detail here: https://github.com/drieslab/Giotto/issues/500#issuecomment-1396083446