filter_scExp {ChromSCape} | R Documentation |
Function to filter out cells & features from SingleCellExperiment based on total count per cell, number of cells 'ON' in features and top covered cells that might be doublets.
filter_scExp( scExp, min_cov_cell = 1600, quant_removal = 95, min_count_per_feature = 10, verbose = TRUE )
scExp |
A SingleCellExperiment object. |
min_cov_cell |
Minimum counts for each cell. (1600) |
quant_removal |
Centile of cell counts above which cells are removed. (95) |
min_count_per_feature |
Minimum number of reads per feature (10). |
verbose |
(TRUE) |
Returns a filtered SingleCellExperiment object.
raw <- create_scDataset_raw() scExp = create_scExp(raw$mat, raw$annot) scExp. = filter_scExp(scExp) # No feature filtering (all features are valuable) scExp. = filter_scExp(scExp,min_count_per_feature=30) # No cell filtering (all features are valuable) scExp. = filter_scExp(scExp,min_cov_cell=0,quant_removal=100)