Compute seismic specificity score for each gene and cell type.
Source:R/calc_specificity.R
calc_specificity.RdCompute seismic specificity score for each gene and cell type.
Usage
calc_specificity(
sce,
assay_name = "logcounts",
ct_label_col = "idents",
min_uniq_ct = 2,
min_ct_size = 20,
min_cells_gene_exp = 10,
min_avg_exp_ct = 0.1
)Arguments
- sce
A SingleCellExperiment object. This object needs to include the assay_name specified and a ct_label_col column corresponding to cell type labels for the granularity of interest. Row names are used as the gene name identifiers.
- assay_name
An assay in sce, default 'logcounts' (calculated using scran).
- ct_label_col
A column name in colData of sce (information for the cells in sce) that provides labels for each cell, indicating membership in each cell type at the granularity of interest.
- min_uniq_ct
The minimum number of unique cell types needed in the data to proceed with specificity score calculations. Default: 2.
- min_ct_size
Filter for cell types to be included in the specificity score calculation based on the number of cells that are labeled as that cell type. Default: 20.
- min_cells_gene_exp
Filter for genes to be included in the specificity score calculation based on the number of cells where the gene has non-zero expression. Default: 10.
- min_avg_exp_ct
Filter for genes to be included in the specificity score calculation based on the mean of cell-type-averaged expressions (aka mean of mean cell type expression). Default: 0.1