aggregate_mapped_genes: Aggregate/expand a gene matrix by gene mappings

In neurogenomics/orthogene: Interspecies gene mapping

Aggregate/expand a gene matrix by gene mappings

Description

Aggregate/expand a gene matrix (gene_df) using a gene mapping data.frame (gene_map). Importantly, mappings can be performed across a variety of scenarios that can occur during within-species and between-species gene mapping:

• 1 gene : 1 gene

• many genes : 1 gene

• 1 gene : many genes

• many genes : many genes

For more details on how aggregation/expansion is performed, please see: many2many_rows.

Usage

aggregate_mapped_genes(
  gene_df,
  gene_map = NULL,
  input_col = "input_gene",
  output_col = "ortholog_gene",
  input_species = "human",
  output_species = input_species,
  method = c("gprofiler", "homologene", "babelgene"),
  agg_fun = "sum",
  agg_method = c("monocle3", "stats"),
  aggregate_orthologs = TRUE,
  transpose = FALSE,
  mthreshold = 1,
  target = "ENSG",
  numeric_ns = "",
  as_integers = FALSE,
  as_sparse = TRUE,
  as_DelayedArray = FALSE,
  dropNA = TRUE,
  sort_rows = FALSE,
  verbose = TRUE
)

Arguments

gene_df	Input matrix where row names are genes.
gene_map	A data.frame that maps the current gene names to new gene names. This function's behaviour will adapt to different situations as follows: gene_map=<data.frame> : When a data.frame containing the gene key:value columns (specified by input_col and output_col, respectively) is provided, this will be used to perform aggregation/expansion. gene_map=NULL and input_species!=output_species : A gene_map is automatically generated by map_orthologs to perform inter-species gene aggregation/expansion. gene_map=NULL and input_species==output_species : A gene_map is automatically generated by map_genes to perform within-species gene gene symbol standardization and aggregation/expansion.
input_col	Column name within gene_map with gene names matching the row names of X.
output_col	Column name within gene_map with gene names that you wish you map the row names of X onto.
input_species	Name of the input species (e.g., "mouse","fly"). Use map_species to return a full list of available species.
output_species	Name of the output species (e.g. "human","chicken"). Use map_species to return a full list of available species.
method	R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
agg_fun	Aggregation function.
agg_method	Aggregation method.
aggregate_orthologs	[Optional] After performing an initial round of many:many aggregation/expansion with many2many_rows, ensure each orthologous gene only appears in one row by using the aggregate_rows function (default: TRUE).
transpose	Transpose gene_df before mapping genes.
mthreshold	maximum number of results per initial alias to show. Shows all by default.
target	target namespace.
numeric_ns	namespace to use for fully numeric IDs (list of available namespaces).
as_integers	Force all values in the matrix to become integers, by applying floor (default: FALSE).
as_sparse	Convert aggregated matrix to sparse matrix.
as_DelayedArray	Convert aggregated matrix to DelayedArray.
dropNA	Drop genes assigned to NA in groupings.
sort_rows	Sort gene_df rows alphanumerically.
verbose	Print messages.

Value

Aggregated matrix

Examples

#### Aggregate within species: gene synonyms ####
data("exp_mouse_enst")                                
X_agg <- aggregate_mapped_genes(gene_df = exp_mouse_enst, 
                                input_species = "mouse")  
                                 
#### Aggregate across species: gene orthologs ####               
data("exp_mouse")
X_agg2 <- aggregate_mapped_genes(gene_df = exp_mouse, 
                                 input_species = "mouse",
                                 output_species = "human",
                                 method="homologene")                                                     

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