aggregate_mapped_genes {orthogene} | R Documentation |
Aggregate a gene matrix by gene symbols
Description
Map matrix rownames to standardised gene symbols,
and then aggregate many-to-one rows into a new matrix.
Usage
aggregate_mapped_genes(
gene_df,
species = "human",
FUN = "sum",
method = c("monocle3", "stats", "delayedarray"),
transpose = FALSE,
gene_map = NULL,
gene_map_col = "name",
non121_strategy = "drop_output_species",
as_sparse = TRUE,
as_DelayedArray = FALSE,
dropNA = TRUE,
sort_rows = FALSE,
verbose = TRUE
)
Arguments
gene_df |
Input matrix where row names are genes.
|
species |
Species to map against.
|
FUN |
Aggregation function (DEFAULT: "sum" ).
|
method |
Aggregation method.
|
transpose |
Transpose gene_df before mapping genes.
|
gene_map |
A user-supplied gene_map .
If NULL (DEFAULT)),
map_genes will be used to create a gene_map .
|
gene_map_col |
Column in gene_map to aggregate
gene_df by.
|
non121_strategy |
How to handle genes that don't have
1:1 mappings between input_species :output_species .
Options include:
"drop_both_species" or "dbs" or 1 :
Drop genes that have duplicate
mappings in either the input_species or output_species
(DEFAULT).
"drop_input_species" or "dis" or 2 :
Only drop genes that have duplicate
mappings in the input_species .
"drop_output_species" or "dos" or 3 :
Only drop genes that have duplicate
mappings in the output_species .
"keep_both_species" or "kbs" or 4 :
Keep all genes regardless of whether
they have duplicate mappings in either species.
"keep_popular" or "kp" or 5 :
Return only the most "popular" interspecies ortholog mappings.
This procedure tends to yield a greater number of returned genes
but at the cost of many of them not being true biological 1:1 orthologs.
"sum","mean","median","min" or "max" :
When gene_df is a matrix and gene_output="rownames" ,
these options will aggregate many-to-one gene mappings
(input_species -to-output_species )
after dropping any duplicate genes in the output_species .
|
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
data("exp_mouse")
X_agg <- aggregate_mapped_genes(gene_df = exp_mouse, species = "mouse")
[Package
orthogene version 0.99.9
Index]