Scans the row names of a
SingleCellExperiment object to identify
genes matching specific patterns (e.g. mitochondrial or ribosomal) and
formats them for use in downstream quality control filtering.
Usage
find_qc_features(
sce,
group_configs = list(mito = list(pattern = "^MT-", max_pct = 20), ribo = list(pattern =
"^RP[SL]", max_pct = 50))
)
Arguments
- sce
A SingleCellExperiment object.
- group_configs
A named list of configurations. Each element must be a
list containing:
- pattern
A regex string to match gene names (e.g. "^MT-").
- max_pct
Numeric scalar. The maximum allowed percentage for this
group, carried forward for use in QC filtering.
Defaults to mitochondrial (^MT-, 20%) and ribosomal (^RP[SL], 50%) genes.
Value
A named list where each element contains:
- features
Character vector of matching gene names found in the
object. Empty character vector if no genes matched.
- max_pct
Numeric threshold carried over from the config.
Examples
if (FALSE) { # \dontrun{
# Default usage
qc_feats <- find_qc_features(sce)
# Custom patterns (e.g. hemoglobin genes)
qc_feats <- find_qc_features(sce, group_configs = list(
hb = list(pattern = "^HB[AB]", max_pct = 5)
))
} # }
