Filter the current VariableFeatures() of a Seurat object and drop
genes matching user-defined regular-expression patterns. Default setting (mitochondria / ribosome / TCR / hemoglobin).
Usage
remove_unwant_hvg(
srt,
pattern_list = list(mitochondrial_genes = "^MT-", ribosomal_genes = "^(RPL|RPS)",
tcr_genes = "^TR[ABDG]", hemoglobin_genes = "^HB[AB]")
)Arguments
- srt
A Seurat object with HVGs already defined (e.g. after
FindVariableFeatures()).- pattern_list
Named list of regex patterns. Default
mitochondrial_genes = "^MT-"ribosomal_genes = "^(RPL|RPS)"tcr_genes = "^TR[ABDG]"hemoglobin_genes = "^HB[AB]"
Value
Seurat object with filtered VariableFeatures().
A concise summary is printed.
Examples
if (FALSE) { # \dontrun{
srt <- NormalizeData(srt) |>
FindVariableFeatures(nfeatures = 2000) |>
remove_unwant_hvg()
} # }