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, percentMin = 1, bin_min_count = 2, 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) |
percentMin |
Minimum percent of cells 'ON' in feature. (1) |
bin_min_count |
Minimum number of counts to define if cell is 'ON'. (2) |
verbose |
(TRUE) |
Returns a filtered SingleCellExperiment object.
scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot) scExp. = filter_scExp(scExp) # No feature filtering (all features are valuable) scExp. = filter_scExp(scExp,percentMin=0) # No cell filtering (all features are valuable) scExp. = filter_scExp(scExp,min_cov_cell=0,quant_removal=100)