Extracts dense normalised (log1p) expression values for a set of genes,
optionally with additional observation metadata columns.
Usage
extract_gene_expression(
object,
features,
obs_cols = NULL,
scale = FALSE,
clip = NULL
)
Arguments
- object
SingleCells class.
- features
Character vector. Gene IDs to extract.
- obs_cols
Optional character vector. Column names from the obs table
to include.
- scale
Boolean. Whether to z-score the expression values.
- clip
Optional numeric. If scale = TRUE, clip z-scores to
[-clip, clip].
Value
A data.table with a cell_id column, one column per gene, and
any requested obs columns.