filterGiotto: filterGiotto

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

gobject	giotto object
expression_values	expression values to use
expression_threshold	threshold to consider a gene expressed
gene_det_in_min_cells	minimum # of cells that need to express a gene
min_det_genes_per_cell	minimum # of genes that need to be detected in a cell
verbose	verbose

Details

The function 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)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.