Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 8 | 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.
1 2 3 4 5 6 7 8 | 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)
|
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