aggregate_rows: Aggregate rows of matrix

In neurogenomics/orthogene: Interspecies gene mapping

Aggregate rows of matrix

Description

Aggregate rows of a matrix for many:1 mappings, using a grouping vector.

Usage

aggregate_rows(
  X,
  groupings,
  agg_fun = "sum",
  agg_method = c("monocle3", "stats"),
  as_sparse = TRUE,
  as_DelayedArray = TRUE,
  dropNA = TRUE,
  verbose = TRUE
)

Arguments

X	Input matrix.
groupings	Gene groups of the same length as nrow(X).
agg_fun	Aggregation function.
agg_method	Aggregation method.
as_sparse	Convert aggregated matrix to sparse matrix.
as_DelayedArray	Convert aggregated matrix to DelayedArray.
dropNA	Drop genes assigned to NA in groupings.
verbose	Print messages.

Value

Aggregated matrix

Source

data("exp_mouse_enst") X <- exp_mouse_enst gene_map <- map_genes(genes = rownames(X),species = "mouse") X_agg <- orthogene:::aggregate_rows(X = X, groupings = gene_map$name) sum(duplicated(rownames(exp_mouse))) # 0 sum(duplicated(rownames(X))) # 1215 sum(duplicated(rownames(X_agg))) # 0

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.