Search Pathways in GO/Reactome Database — SearchDatabase • SeuratExtend

Search for pathways in the GO or Reactome database using a gene name, pathway ID (SetID), or pathway name (SetName).

SearchDatabase(
  item,
  type = c("gene", "SetID", "SetName"),
  database = c("GO", "Reactome"),
  spe = getOption("spe"),
  export.to.data.frame = F,
  n.min = 1,
  n.max = Inf,
  only.end.terms = F,
  return = c("all", "ID", "genelist")
)

Arguments

item: A gene name, pathway ID, or pathway name.
type: Types of search criteria. Can be one or a combination of "gene", "SetID", "SetName". Default: c("gene", "SetID", "SetName").
database: The database to search in: "GO", "Reactome", or both. Default: c("GO", "Reactome").
spe: Species, either 'human' or 'mouse'. Default: getOption("spe").
export.to.data.frame: If TRUE, the results will be returned as a data frame, which can be easily exported to csv or xlsx formats. Default: FALSE.
n.min: Minimum number of genes required in the gene set. Default: 1.
n.max: Maximum number of genes allowed in the gene set. Default: Inf.
only.end.terms: If TRUE, only the end-level pathways or gene sets will be returned. Default: FALSE.
return: Specifies the format of the result. If set to "all" (default), the result will include all information (pathway ID, pathway name, genes). If set to "ID", it will only return a vector of pathway IDs. If set to "genelist", it will return a list where the names are pathway IDs and the contents are the corresponding genes.

Value

Depending on the specified parameters, the function returns:

A full list (with pathway ID, pathway name, and genes) if return = "all".
A vector of pathway IDs if return = "ID".
A named list of genes with pathway IDs as the list names if return = "genelist".
A data frame if export.to.data.frame = TRUE.

Details

Further details and usage can be seen in the provided examples.

Examples

library(SeuratExtend)
library(dplyr)
options(max.print = 10)

# Set the default database search to 'human'
options(spe = "human")

# The 'item' parameter can be anything like a gene, pathway ID, or pathway name.
# For example, search in the GO/Reactome database for pathways that contain the "CD3D" gene
# or pathway names that include "metabolic".
result <- SearchDatabase(c("CD3D","metabolic"))
names(result)
glimpse(head(result, 5))

# If you only want to search based on gene names, you can specify this in the 'type' parameter.
result <- SearchDatabase("CD3D", type = "gene")
names(result)

# If you want to search in a specific database, you can specify it using the 'database' parameter.
result <- SearchDatabase("CD3D", database = "Reactome")
names(result)

# You can specify the database to be either 'human' or 'mouse' using the 'spe' parameter.
result <- SearchDatabase("Cd3d", spe = "mouse")
glimpse(head(result, 5))

# If you only want the result to be a list of pathway IDs, which could be useful for subsequent analysis,
# you can set the 'return' parameter accordingly.
result <- SearchDatabase("CD3D", return = "ID")
result

# If you want the output as a gene list, with the IDs as names, suitable for inputs like GeneSetAnalysis,
# you can adjust the 'return' parameter.
result <- SearchDatabase("CD3D", return = "genelist")
glimpse(head(result, 5))

# If you prefer the output to be a data frame, which is suitable for exporting to Excel or CSV formats,
# you can set 'export.to.data.frame' to TRUE.
result <- SearchDatabase("CD3D", export.to.data.frame = TRUE)
glimpse(result)