runGeneralQC {rliger} | R Documentation |
General QC for liger object
Description
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 |
mito , ribo , hemo |
Whether to calculate the expression percentage of
mitochondrial, ribosomal or hemoglobin genes, respectively. Default
|
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 |
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 |
useDatasets |
A character vector of the names, a numeric or logical
vector of the index of the datasets to be included for QC. Default
|
chunkSize |
Integer number of cells to include in a chunk when working
on HDF5 based dataset. Default |
verbose |
Logical. Whether to show information of the progress. Default
|
Value
Updated object
with nUMI
, nGene
updated
in cellMeta(object)
, as well as expression percentage value for each
feature subset.
Examples
pbmc <- runGeneralQC(pbmc)