Filter Giotto

filterGiotto()

Filter Giotto object based on expression threshold.

createGiottoVisiumObject(
    visium_dir = NULL,
     expr_data = c("raw", "filter"),
    gene_column_index = 1,
    h5_visium_path = NULL,
    h5_gene_ids = c("symbols", "ensembl"),
    h5_tissue_positions_path = NULL,
    h5_image_png_path = NULL,
    png_name = NULL,
    xmax_adj = 0,
    xmin_adj = 0,
    ymax_adj = 0,
    ymin_adj = 0,
    instructions = NULL,
    cores = NA,
    verbose = TRUE
)

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

Value

Giotto Object

Details

The function filterCombinations can be used to explore the effect of different parameter values.

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)