Calculate number of UMIs, number of detected features and percentage of feature subset (e.g. mito) expression per cell.
Usage
runGeneralQC(
object,
mito = TRUE,
ribo = TRUE,
hemo = TRUE,
features = NULL,
pattern = NULL,
useDatasets = NULL,
chunkSize = 1000,
verbose = getOption("ligerVerbose", TRUE)
)
Arguments
- object
liger object with
rawData
available in each ligerDataset embedded- mito, ribo, hemo
Whether to calculate the expression percentage of mitochondrial, ribosomal or hemoglobin genes, respectively. Default
TRUE
.- features
Feature names matching the feature subsets that users want to calculate the expression percentage with. A vector for a single subset, or a named list for multiple subset. Default
NULL
.- pattern
Regex patterns for matching the feature subsets that users want to calculate the expression percentage with. A vector for a single subset, or a named list for multiple subset. Default
NULL
.- useDatasets
A character vector of the names, a numeric or logical vector of the index of the datasets to be included for QC. Default
NULL
performs QC on all datasets.- chunkSize
Integer number of cells to include in a chunk when working on HDF5 based dataset. Default
1000
- verbose
Logical. Whether to show information of the progress. Default
getOption("ligerVerbose")
orTRUE
if users have not set.