R: Aggregate a gene matrix by gene symbols

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 1.0.2 Index]